Starting phenix.real_space_refine on Wed Aug 5 10:26:34 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9k9l_62193/08_2026/9k9l_62193.cif Found real_map, /net/cci-nas-00/data/ceres_data/9k9l_62193/08_2026/9k9l_62193.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.66 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9k9l_62193/08_2026/9k9l_62193.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9k9l_62193/08_2026/9k9l_62193.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9k9l_62193/08_2026/9k9l_62193.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9k9l_62193/08_2026/9k9l_62193.map" } resolution = 3.66 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.006 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 P 242 5.49 5 S 8 5.16 5 C 5446 2.51 5 N 1855 2.21 5 O 2262 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 31 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 9813 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 621 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 621 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 2, 'TRANS': 73} Chain: "B" Number of atoms: 587 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 587 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 1, 'TRANS': 71} Chain: "C" Number of atoms: 628 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 628 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 2, 'TRANS': 74} Chain: "D" Number of atoms: 587 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 587 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 1, 'TRANS': 71} Chain: "E" Number of atoms: 634 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 634 Classifications: {'peptide': 78} Link IDs: {'PTRANS': 2, 'TRANS': 75} Chain: "F" Number of atoms: 587 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 587 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 1, 'TRANS': 71} Chain: "G" Number of atoms: 621 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 621 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 2, 'TRANS': 73} Chain: "H" Number of atoms: 587 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 587 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 1, 'TRANS': 71} Chain: "I" Number of atoms: 2463 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 2463 Classifications: {'DNA': 121} Link IDs: {'rna3p': 120} Chain: "J" Number of atoms: 2498 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 2498 Classifications: {'DNA': 121} Link IDs: {'rna3p': 120} Time building chain proxies: 1.42, per 1000 atoms: 0.14 Number of scatterers: 9813 At special positions: 0 Unit cell: (111.3, 118.72, 100.7, 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) S 8 16.00 P 242 15.00 O 2262 8.00 N 1855 7.00 C 5446 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.97 Conformation dependent library (CDL) restraints added in 165.0 milliseconds 1166 Ramachandran restraints generated. 583 Oldfield, 0 Emsley, 583 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1126 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 7 sheets defined 79.8% alpha, 2.3% beta 120 base pairs and 184 stacking pairs defined. Time for finding SS restraints: 1.19 Creating SS restraints... Processing helix chain 'A' and resid 63 through 80 Processing helix chain 'A' and resid 87 through 116 Processing helix chain 'A' and resid 122 through 134 removed outlier: 3.781A pdb=" N VAL A 126 " --> pdb=" O PHE A 122 " (cutoff:3.500A) Processing helix chain 'B' and resid 24 through 29 removed outlier: 3.517A pdb=" N ILE B 29 " --> pdb=" O ILE B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 41 Processing helix chain 'B' and resid 49 through 76 Processing helix chain 'B' and resid 82 through 94 Processing helix chain 'C' and resid 63 through 79 removed outlier: 3.532A pdb=" N PHE C 67 " --> pdb=" O ARG C 63 " (cutoff:3.500A) Processing helix chain 'C' and resid 87 through 116 Processing helix chain 'C' and resid 122 through 134 removed outlier: 3.869A pdb=" N VAL C 126 " --> pdb=" O PHE C 122 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N GLN C 127 " --> pdb=" O PRO C 123 " (cutoff:3.500A) Processing helix chain 'D' and resid 24 through 29 removed outlier: 3.551A pdb=" N ILE D 29 " --> pdb=" O ILE D 26 " (cutoff:3.500A) Processing helix chain 'D' and resid 30 through 41 Processing helix chain 'D' and resid 49 through 76 Processing helix chain 'D' and resid 82 through 94 Processing helix chain 'E' and resid 63 through 80 removed outlier: 3.504A pdb=" N PHE E 78 " --> pdb=" O ILE E 74 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N THR E 79 " --> pdb=" O CYS E 75 " (cutoff:3.500A) Processing helix chain 'E' and resid 87 through 116 removed outlier: 3.502A pdb=" N ALA E 116 " --> pdb=" O LEU E 112 " (cutoff:3.500A) Processing helix chain 'E' and resid 122 through 134 removed outlier: 3.553A pdb=" N VAL E 126 " --> pdb=" O PHE E 122 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ALA E 129 " --> pdb=" O ASP E 125 " (cutoff:3.500A) Processing helix chain 'F' and resid 24 through 29 Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 49 through 76 Processing helix chain 'F' and resid 82 through 94 Processing helix chain 'G' and resid 63 through 79 removed outlier: 3.628A pdb=" N PHE G 67 " --> pdb=" O ARG G 63 " (cutoff:3.500A) Processing helix chain 'G' and resid 87 through 116 Processing helix chain 'G' and resid 122 through 134 Processing helix chain 'H' and resid 24 through 29 Processing helix chain 'H' and resid 30 through 41 Processing helix chain 'H' and resid 49 through 76 Processing helix chain 'H' and resid 82 through 94 Processing sheet with id=AA1, first strand: chain 'A' and resid 85 through 86 removed outlier: 6.877A pdb=" N ASN A 85 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 120 through 121 removed outlier: 3.705A pdb=" N LEU A 121 " --> pdb=" O ARG B 45 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'C' and resid 85 through 86 removed outlier: 6.652A pdb=" N ASN C 85 " --> pdb=" O VAL D 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'E' and resid 85 through 86 removed outlier: 6.763A pdb=" N ASN E 85 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'E' and resid 120 through 121 Processing sheet with id=AA6, first strand: chain 'G' and resid 85 through 86 removed outlier: 6.801A pdb=" N ASN G 85 " --> pdb=" O VAL H 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'G' and resid 120 through 121 360 hydrogen bonds defined for protein. 1050 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 312 hydrogen bonds 624 hydrogen bond angles 0 basepair planarities 120 basepair parallelities 184 stacking parallelities Total time for adding SS restraints: 1.10 Time building geometry restraints manager: 1.25 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 1883 1.33 - 1.45: 3461 1.45 - 1.57: 4650 1.57 - 1.69: 482 1.69 - 1.81: 12 Bond restraints: 10488 Sorted by residual: bond pdb=" C3' DC I -48 " pdb=" O3' DC I -48 " ideal model delta sigma weight residual 1.435 1.479 -0.044 1.30e-02 5.92e+03 1.16e+01 bond pdb=" C3' DC J -27 " pdb=" C2' DC J -27 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.81e+00 bond pdb=" C3' DC I 20 " pdb=" C2' DC I 20 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.71e+00 bond pdb=" C3' DC I -8 " pdb=" C2' DC I -8 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.48e+00 bond pdb=" C3' DT I 55 " pdb=" C2' DT I 55 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 9.28e+00 ... (remaining 10483 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.46: 13947 1.46 - 2.91: 1162 2.91 - 4.37: 66 4.37 - 5.82: 25 5.82 - 7.28: 3 Bond angle restraints: 15203 Sorted by residual: angle pdb=" N3 DT J 7 " pdb=" C4 DT J 7 " pdb=" O4 DT J 7 " ideal model delta sigma weight residual 119.90 122.78 -2.88 6.00e-01 2.78e+00 2.31e+01 angle pdb=" O4' DT J 12 " pdb=" C4' DT J 12 " pdb=" C3' DT J 12 " ideal model delta sigma weight residual 106.00 103.26 2.74 6.00e-01 2.78e+00 2.08e+01 angle pdb=" N3 DT J -26 " pdb=" C4 DT J -26 " pdb=" O4 DT J -26 " ideal model delta sigma weight residual 119.90 122.54 -2.64 6.00e-01 2.78e+00 1.93e+01 angle pdb=" O4 DT J 7 " pdb=" C4 DT J 7 " pdb=" C5 DT J 7 " ideal model delta sigma weight residual 124.90 121.84 3.06 7.00e-01 2.04e+00 1.91e+01 angle pdb=" N3 DT J 29 " pdb=" C4 DT J 29 " pdb=" O4 DT J 29 " ideal model delta sigma weight residual 119.90 122.48 -2.58 6.00e-01 2.78e+00 1.85e+01 ... (remaining 15198 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.92: 4356 32.92 - 65.83: 1211 65.83 - 98.75: 35 98.75 - 131.67: 1 131.67 - 164.58: 3 Dihedral angle restraints: 5606 sinusoidal: 3873 harmonic: 1733 Sorted by residual: dihedral pdb=" C4' DC I 51 " pdb=" C3' DC I 51 " pdb=" O3' DC I 51 " pdb=" P DA I 52 " ideal model delta sinusoidal sigma weight residual 220.00 55.42 164.58 1 3.50e+01 8.16e-04 1.54e+01 dihedral pdb=" C4' DT I 14 " pdb=" C3' DT I 14 " pdb=" O3' DT I 14 " pdb=" P DT I 15 " ideal model delta sinusoidal sigma weight residual 220.00 59.11 160.89 1 3.50e+01 8.16e-04 1.52e+01 dihedral pdb=" C4' DC I -48 " pdb=" C3' DC I -48 " pdb=" O3' DC I -48 " pdb=" P DG I -47 " ideal model delta sinusoidal sigma weight residual 220.00 64.50 155.50 1 3.50e+01 8.16e-04 1.50e+01 ... (remaining 5603 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.111: 1710 0.111 - 0.221: 21 0.221 - 0.332: 1 0.332 - 0.443: 0 0.443 - 0.553: 1 Chirality restraints: 1733 Sorted by residual: chirality pdb=" P DC I 51 " pdb=" OP1 DC I 51 " pdb=" OP2 DC I 51 " pdb=" O5' DC I 51 " both_signs ideal model delta sigma weight residual True 2.34 -2.89 -0.55 2.00e-01 2.50e+01 7.65e+00 chirality pdb=" CB ILE H 46 " pdb=" CA ILE H 46 " pdb=" CG1 ILE H 46 " pdb=" CG2 ILE H 46 " both_signs ideal model delta sigma weight residual False 2.64 2.39 0.26 2.00e-01 2.50e+01 1.65e+00 chirality pdb=" CB ILE H 26 " pdb=" CA ILE H 26 " pdb=" CG1 ILE H 26 " pdb=" CG2 ILE H 26 " both_signs ideal model delta sigma weight residual False 2.64 2.44 0.20 2.00e-01 2.50e+01 1.01e+00 ... (remaining 1730 not shown) Planarity restraints: 1077 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU C 107 " 0.014 2.00e-02 2.50e+03 2.83e-02 8.00e+00 pdb=" C GLU C 107 " -0.049 2.00e-02 2.50e+03 pdb=" O GLU C 107 " 0.018 2.00e-02 2.50e+03 pdb=" N ASP C 108 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG D 78 " 0.241 9.50e-02 1.11e+02 1.08e-01 7.15e+00 pdb=" NE ARG D 78 " -0.014 2.00e-02 2.50e+03 pdb=" CZ ARG D 78 " -0.003 2.00e-02 2.50e+03 pdb=" NH1 ARG D 78 " -0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG D 78 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE B 50 " 0.012 2.00e-02 2.50e+03 2.33e-02 5.43e+00 pdb=" C ILE B 50 " -0.040 2.00e-02 2.50e+03 pdb=" O ILE B 50 " 0.015 2.00e-02 2.50e+03 pdb=" N TYR B 51 " 0.014 2.00e-02 2.50e+03 ... (remaining 1074 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 1756 2.78 - 3.31: 9056 3.31 - 3.84: 19758 3.84 - 4.37: 22053 4.37 - 4.90: 31413 Nonbonded interactions: 84036 Sorted by model distance: nonbonded pdb=" OE2 GLU B 63 " pdb=" NZ LYS F 91 " model vdw 2.253 3.120 nonbonded pdb=" OG SER C 68 " pdb=" NH2 ARG C 72 " model vdw 2.259 3.120 nonbonded pdb=" O LEU C 61 " pdb=" NH2 ARG D 36 " model vdw 2.291 3.120 nonbonded pdb=" NH2 ARG G 72 " pdb=" OP1 DC I 8 " model vdw 2.298 3.120 nonbonded pdb=" N VAL A 119 " pdb=" OP1 DC J 28 " model vdw 2.325 3.120 ... (remaining 84031 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: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'C' and resid 59 through 134) selection = (chain 'E' and resid 59 through 134) selection = chain 'G' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' selection = chain 'H' } 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 group one per residue 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: 0.460 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: 0.030 Set scattering table: 0.020 Process input model: 8.300 Find NCS groups from input model: 0.110 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:1.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7468 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 0.044 10488 Z= 0.528 Angle : 0.810 7.280 15203 Z= 0.702 Chirality : 0.048 0.553 1733 Planarity : 0.006 0.108 1077 Dihedral : 28.694 164.584 4480 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.69 % Favored : 99.31 % Rotamer: Outliers : 0.80 % Allowed : 4.41 % Favored : 94.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.22 (0.29), residues: 583 helix: 0.48 (0.20), residues: 473 sheet: None (None), residues: 0 loop : -0.88 (0.43), residues: 110 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG E 130 TYR 0.018 0.002 TYR D 88 PHE 0.018 0.002 PHE E 106 TRP 0.003 0.001 TRP C 86 HIS 0.002 0.001 HIS E 115 Details of bonding type rmsd/Z covalent geometry : bond 0.00598 / 0.53 (10488) covalent geometry : angle 0.80999 / 0.70 (15203) hydrogen bonds : bond 0.10569 / 7.04 ( 672) hydrogen bonds : angle 3.60412 / 2.59 ( 1674) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1166 Ramachandran restraints generated. 583 Oldfield, 0 Emsley, 583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1166 Ramachandran restraints generated. 583 Oldfield, 0 Emsley, 583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 81 time to evaluate : 0.228 Fit side-chains revert: symmetry clash REVERT: E 78 PHE cc_start: 0.7743 (m-80) cc_final: 0.7333 (m-80) REVERT: E 85 ASN cc_start: 0.8309 (m-40) cc_final: 0.8030 (m-40) REVERT: G 80 ARG cc_start: 0.7452 (mtm-85) cc_final: 0.7044 (ptp90) REVERT: H 91 LYS cc_start: 0.7721 (tttt) cc_final: 0.7345 (mttt) REVERT: H 93 GLN cc_start: 0.7574 (tm-30) cc_final: 0.7269 (tm-30) outliers start: 4 outliers final: 0 residues processed: 83 average time/residue: 0.1592 time to fit residues: 15.7550 Evaluate side-chains 56 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 56 time to evaluate : 0.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 49 optimal weight: 0.8980 chunk 53 optimal weight: 0.5980 chunk 5 optimal weight: 0.8980 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 9.9990 chunk 62 optimal weight: 20.0000 chunk 51 optimal weight: 0.5980 chunk 38 optimal weight: 0.9980 chunk 61 optimal weight: 20.0000 chunk 45 optimal weight: 0.9990 chunk 74 optimal weight: 10.0000 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 27 GLN C 85 ASN D 27 GLN E 115 HIS ** G 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 75 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4382 r_free = 0.4382 target = 0.215860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.160265 restraints weight = 11748.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.157874 restraints weight = 23125.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.159311 restraints weight = 18202.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.159908 restraints weight = 13179.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.160622 restraints weight = 12845.147| |-----------------------------------------------------------------------------| r_work (final): 0.3779 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7461 moved from start: 0.0971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10488 Z= 0.165 Angle : 0.633 6.222 15203 Z= 0.382 Chirality : 0.045 0.313 1733 Planarity : 0.005 0.049 1077 Dihedral : 32.022 175.684 3289 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.34 % Favored : 99.66 % Rotamer: Outliers : 0.80 % Allowed : 8.42 % Favored : 90.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.46 (0.32), residues: 583 helix: 2.33 (0.23), residues: 456 sheet: None (None), residues: 0 loop : -1.04 (0.40), residues: 127 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 35 TYR 0.009 0.002 TYR D 88 PHE 0.012 0.001 PHE E 106 TRP 0.003 0.001 TRP E 86 HIS 0.004 0.001 HIS A 115 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.16 (10488) covalent geometry : angle 0.63287 / 0.38 (15203) hydrogen bonds : bond 0.05744 / 3.78 ( 672) hydrogen bonds : angle 3.03030 / 2.20 ( 1674) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1166 Ramachandran restraints generated. 583 Oldfield, 0 Emsley, 583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1166 Ramachandran restraints generated. 583 Oldfield, 0 Emsley, 583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 56 time to evaluate : 0.239 Fit side-chains revert: symmetry clash REVERT: F 92 ARG cc_start: 0.7261 (ttp80) cc_final: 0.7049 (ttm-80) REVERT: G 80 ARG cc_start: 0.7278 (mtm-85) cc_final: 0.7033 (ptp90) REVERT: H 91 LYS cc_start: 0.7945 (tttt) cc_final: 0.7384 (mttt) REVERT: H 93 GLN cc_start: 0.7761 (tm-30) cc_final: 0.7532 (tm-30) outliers start: 4 outliers final: 1 residues processed: 59 average time/residue: 0.1191 time to fit residues: 8.9502 Evaluate side-chains 52 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 51 time to evaluate : 0.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 82 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 44 optimal weight: 3.9990 chunk 51 optimal weight: 0.0970 chunk 13 optimal weight: 0.7980 chunk 40 optimal weight: 3.9990 chunk 74 optimal weight: 20.0000 chunk 18 optimal weight: 1.9990 chunk 49 optimal weight: 3.9990 chunk 64 optimal weight: 20.0000 chunk 36 optimal weight: 0.9990 chunk 32 optimal weight: 0.9980 chunk 45 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 27 GLN D 27 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4402 r_free = 0.4402 target = 0.217631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.154117 restraints weight = 11769.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.151981 restraints weight = 16796.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.153402 restraints weight = 14838.683| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.154298 restraints weight = 11336.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.155066 restraints weight = 10824.742| |-----------------------------------------------------------------------------| r_work (final): 0.3653 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7597 moved from start: 0.1407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 10488 Z= 0.150 Angle : 0.596 6.026 15203 Z= 0.360 Chirality : 0.043 0.353 1733 Planarity : 0.004 0.040 1077 Dihedral : 32.156 173.516 3289 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Rotamer: Outliers : 2.00 % Allowed : 9.82 % Favored : 88.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.97 (0.33), residues: 583 helix: 2.70 (0.23), residues: 456 sheet: None (None), residues: 0 loop : -0.94 (0.41), residues: 127 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 67 TYR 0.010 0.002 TYR D 72 PHE 0.011 0.001 PHE E 67 TRP 0.016 0.002 TRP C 86 HIS 0.003 0.001 HIS H 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.15 (10488) covalent geometry : angle 0.59611 / 0.36 (15203) hydrogen bonds : bond 0.05130 / 3.36 ( 672) hydrogen bonds : angle 2.80257 / 2.04 ( 1674) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1166 Ramachandran restraints generated. 583 Oldfield, 0 Emsley, 583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1166 Ramachandran restraints generated. 583 Oldfield, 0 Emsley, 583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 60 time to evaluate : 0.142 Fit side-chains revert: symmetry clash REVERT: B 84 MET cc_start: 0.7016 (mmt) cc_final: 0.6790 (tpp) REVERT: B 92 ARG cc_start: 0.7495 (ttp80) cc_final: 0.7200 (ttm-80) REVERT: D 50 ILE cc_start: 0.8446 (OUTLIER) cc_final: 0.8102 (tp) REVERT: G 80 ARG cc_start: 0.7320 (mtm-85) cc_final: 0.7082 (ptp90) REVERT: H 91 LYS cc_start: 0.7961 (tttt) cc_final: 0.7651 (ttmt) REVERT: H 92 ARG cc_start: 0.5925 (tpt90) cc_final: 0.5482 (tpp-160) outliers start: 10 outliers final: 6 residues processed: 68 average time/residue: 0.1238 time to fit residues: 10.7609 Evaluate side-chains 59 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 52 time to evaluate : 0.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain D residue 50 ILE Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain H residue 50 ILE Chi-restraints excluded: chain H residue 82 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 42 optimal weight: 3.9990 chunk 22 optimal weight: 3.9990 chunk 39 optimal weight: 0.9990 chunk 74 optimal weight: 20.0000 chunk 58 optimal weight: 20.0000 chunk 77 optimal weight: 20.0000 chunk 44 optimal weight: 3.9990 chunk 71 optimal weight: 20.0000 chunk 68 optimal weight: 30.0000 chunk 53 optimal weight: 0.9980 chunk 79 optimal weight: 40.0000 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 27 GLN G 95 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4233 r_free = 0.4233 target = 0.199158 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.140095 restraints weight = 11985.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.140626 restraints weight = 27611.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.141938 restraints weight = 18842.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.142818 restraints weight = 13226.413| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.143441 restraints weight = 12127.495| |-----------------------------------------------------------------------------| r_work (final): 0.3586 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7762 moved from start: 0.2609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.070 10488 Z= 0.277 Angle : 0.809 9.005 15203 Z= 0.443 Chirality : 0.051 0.366 1733 Planarity : 0.006 0.048 1077 Dihedral : 32.577 179.423 3289 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 4.21 % Allowed : 13.43 % Favored : 82.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.70 (0.32), residues: 583 helix: 1.76 (0.23), residues: 459 sheet: None (None), residues: 0 loop : -1.28 (0.44), residues: 124 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG H 40 TYR 0.034 0.003 TYR D 88 PHE 0.017 0.002 PHE E 78 TRP 0.014 0.002 TRP C 86 HIS 0.012 0.002 HIS H 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00632 / 0.28 (10488) covalent geometry : angle 0.80898 / 0.44 (15203) hydrogen bonds : bond 0.07121 / 4.69 ( 672) hydrogen bonds : angle 3.22733 / 2.34 ( 1674) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1166 Ramachandran restraints generated. 583 Oldfield, 0 Emsley, 583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1166 Ramachandran restraints generated. 583 Oldfield, 0 Emsley, 583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 69 time to evaluate : 0.159 Fit side-chains REVERT: F 80 THR cc_start: 0.8006 (OUTLIER) cc_final: 0.7691 (t) REVERT: G 60 LEU cc_start: 0.8315 (OUTLIER) cc_final: 0.8058 (mt) REVERT: G 80 ARG cc_start: 0.7297 (mtm-85) cc_final: 0.6983 (ptp90) REVERT: H 92 ARG cc_start: 0.6492 (tpt90) cc_final: 0.5958 (tpp-160) outliers start: 21 outliers final: 9 residues processed: 86 average time/residue: 0.1204 time to fit residues: 13.2051 Evaluate side-chains 69 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 58 time to evaluate : 0.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain F residue 84 MET Chi-restraints excluded: chain G residue 60 LEU Chi-restraints excluded: chain G residue 79 THR Chi-restraints excluded: chain H residue 50 ILE Chi-restraints excluded: chain H residue 82 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 32 optimal weight: 0.7980 chunk 42 optimal weight: 1.9990 chunk 43 optimal weight: 0.8980 chunk 5 optimal weight: 0.6980 chunk 23 optimal weight: 3.9990 chunk 9 optimal weight: 0.9980 chunk 58 optimal weight: 20.0000 chunk 0 optimal weight: 0.9990 chunk 3 optimal weight: 0.5980 chunk 75 optimal weight: 20.0000 chunk 10 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 27 GLN ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 27 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4328 r_free = 0.4328 target = 0.209352 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.146890 restraints weight = 11744.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.148267 restraints weight = 23639.812| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.149647 restraints weight = 20030.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.150032 restraints weight = 13633.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.150831 restraints weight = 13114.930| |-----------------------------------------------------------------------------| r_work (final): 0.3616 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7701 moved from start: 0.2627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 10488 Z= 0.153 Angle : 0.626 7.728 15203 Z= 0.368 Chirality : 0.044 0.370 1733 Planarity : 0.004 0.037 1077 Dihedral : 32.460 179.562 3289 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 3.41 % Allowed : 13.63 % Favored : 82.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.82 (0.32), residues: 583 helix: 2.60 (0.23), residues: 448 sheet: None (None), residues: 0 loop : -0.76 (0.43), residues: 135 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F 78 TYR 0.017 0.002 TYR F 88 PHE 0.009 0.001 PHE E 67 TRP 0.010 0.001 TRP C 86 HIS 0.004 0.001 HIS A 115 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.15 (10488) covalent geometry : angle 0.62595 / 0.37 (15203) hydrogen bonds : bond 0.05212 / 3.39 ( 672) hydrogen bonds : angle 2.85839 / 2.07 ( 1674) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1166 Ramachandran restraints generated. 583 Oldfield, 0 Emsley, 583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1166 Ramachandran restraints generated. 583 Oldfield, 0 Emsley, 583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 56 time to evaluate : 0.142 Fit side-chains REVERT: E 122 PHE cc_start: 0.8705 (OUTLIER) cc_final: 0.8398 (m-80) REVERT: H 92 ARG cc_start: 0.6318 (tpt90) cc_final: 0.5774 (tpp-160) outliers start: 17 outliers final: 10 residues processed: 69 average time/residue: 0.1183 time to fit residues: 10.5898 Evaluate side-chains 65 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 54 time to evaluate : 0.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 112 LEU Chi-restraints excluded: chain D residue 46 ILE Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain E residue 122 PHE Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain G residue 82 VAL Chi-restraints excluded: chain H residue 50 ILE Chi-restraints excluded: chain H residue 82 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 35 optimal weight: 1.9990 chunk 63 optimal weight: 20.0000 chunk 28 optimal weight: 1.9990 chunk 73 optimal weight: 20.0000 chunk 72 optimal weight: 9.9990 chunk 61 optimal weight: 20.0000 chunk 12 optimal weight: 0.6980 chunk 64 optimal weight: 20.0000 chunk 29 optimal weight: 0.6980 chunk 68 optimal weight: 30.0000 chunk 60 optimal weight: 20.0000 overall best weight: 3.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 27 GLN B 75 HIS D 27 GLN ** E 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 115 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4191 r_free = 0.4191 target = 0.195386 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.137776 restraints weight = 11958.354| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.140161 restraints weight = 30396.277| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.140925 restraints weight = 21174.421| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.144057 restraints weight = 13046.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.144221 restraints weight = 10354.219| |-----------------------------------------------------------------------------| r_work (final): 0.3562 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7798 moved from start: 0.3343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.078 10488 Z= 0.282 Angle : 0.770 8.640 15203 Z= 0.424 Chirality : 0.050 0.375 1733 Planarity : 0.006 0.057 1077 Dihedral : 32.750 179.497 3289 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 10.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 2.61 % Allowed : 17.23 % Favored : 80.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.83 (0.33), residues: 583 helix: 1.91 (0.23), residues: 459 sheet: None (None), residues: 0 loop : -1.52 (0.43), residues: 124 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 78 TYR 0.031 0.003 TYR F 88 PHE 0.017 0.002 PHE A 78 TRP 0.009 0.002 TRP C 86 HIS 0.006 0.002 HIS H 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00657 / 0.28 (10488) covalent geometry : angle 0.77016 / 0.42 (15203) hydrogen bonds : bond 0.06829 / 4.47 ( 672) hydrogen bonds : angle 3.14160 / 2.28 ( 1674) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1166 Ramachandran restraints generated. 583 Oldfield, 0 Emsley, 583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1166 Ramachandran restraints generated. 583 Oldfield, 0 Emsley, 583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 58 time to evaluate : 0.193 Fit side-chains REVERT: A 131 ARG cc_start: 0.7736 (ttp-170) cc_final: 0.7494 (ttp-170) REVERT: D 50 ILE cc_start: 0.8583 (OUTLIER) cc_final: 0.8085 (tp) REVERT: E 122 PHE cc_start: 0.8861 (OUTLIER) cc_final: 0.8578 (m-80) REVERT: F 25 ASN cc_start: 0.8438 (OUTLIER) cc_final: 0.8190 (m-40) outliers start: 13 outliers final: 9 residues processed: 71 average time/residue: 0.1171 time to fit residues: 10.9052 Evaluate side-chains 65 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 53 time to evaluate : 0.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 112 LEU Chi-restraints excluded: chain D residue 50 ILE Chi-restraints excluded: chain D residue 70 VAL Chi-restraints excluded: chain E residue 122 PHE Chi-restraints excluded: chain F residue 25 ASN Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain H residue 50 ILE Chi-restraints excluded: chain H residue 82 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 44 optimal weight: 0.6980 chunk 45 optimal weight: 0.9980 chunk 57 optimal weight: 40.0000 chunk 74 optimal weight: 20.0000 chunk 77 optimal weight: 20.0000 chunk 33 optimal weight: 0.5980 chunk 16 optimal weight: 3.9990 chunk 75 optimal weight: 20.0000 chunk 78 optimal weight: 30.0000 chunk 22 optimal weight: 0.8980 chunk 14 optimal weight: 2.9990 overall best weight: 1.2382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 27 GLN D 27 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4216 r_free = 0.4216 target = 0.198358 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.140767 restraints weight = 11833.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.143404 restraints weight = 29031.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.144430 restraints weight = 19788.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.145049 restraints weight = 13419.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.145888 restraints weight = 12204.934| |-----------------------------------------------------------------------------| r_work (final): 0.3604 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7739 moved from start: 0.3393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 10488 Z= 0.167 Angle : 0.640 7.515 15203 Z= 0.371 Chirality : 0.045 0.369 1733 Planarity : 0.004 0.038 1077 Dihedral : 32.685 179.685 3289 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 2.61 % Allowed : 18.04 % Favored : 79.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.42 (0.33), residues: 583 helix: 2.35 (0.23), residues: 459 sheet: None (None), residues: 0 loop : -1.38 (0.44), residues: 124 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 78 TYR 0.020 0.002 TYR F 88 PHE 0.011 0.001 PHE E 67 TRP 0.010 0.001 TRP C 86 HIS 0.002 0.001 HIS A 115 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.17 (10488) covalent geometry : angle 0.63980 / 0.37 (15203) hydrogen bonds : bond 0.05343 / 3.49 ( 672) hydrogen bonds : angle 2.85311 / 2.08 ( 1674) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1166 Ramachandran restraints generated. 583 Oldfield, 0 Emsley, 583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1166 Ramachandran restraints generated. 583 Oldfield, 0 Emsley, 583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 56 time to evaluate : 0.239 Fit side-chains REVERT: B 92 ARG cc_start: 0.7482 (ttp80) cc_final: 0.7089 (ttm170) REVERT: E 122 PHE cc_start: 0.8624 (OUTLIER) cc_final: 0.8306 (m-80) outliers start: 13 outliers final: 9 residues processed: 68 average time/residue: 0.1279 time to fit residues: 11.2809 Evaluate side-chains 63 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 53 time to evaluate : 0.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 112 LEU Chi-restraints excluded: chain D residue 46 ILE Chi-restraints excluded: chain D residue 70 VAL Chi-restraints excluded: chain E residue 122 PHE Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain H residue 50 ILE Chi-restraints excluded: chain H residue 82 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 25 optimal weight: 3.9990 chunk 66 optimal weight: 20.0000 chunk 4 optimal weight: 0.8980 chunk 75 optimal weight: 20.0000 chunk 42 optimal weight: 3.9990 chunk 64 optimal weight: 20.0000 chunk 28 optimal weight: 4.9990 chunk 21 optimal weight: 1.9990 chunk 78 optimal weight: 30.0000 chunk 26 optimal weight: 5.9990 chunk 41 optimal weight: 0.8980 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 27 GLN D 27 GLN ** E 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4180 r_free = 0.4180 target = 0.194701 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.136928 restraints weight = 11931.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.139266 restraints weight = 29717.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.140231 restraints weight = 20193.975| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.143430 restraints weight = 13124.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.143641 restraints weight = 10079.316| |-----------------------------------------------------------------------------| r_work (final): 0.3539 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7807 moved from start: 0.3824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 10488 Z= 0.230 Angle : 0.715 8.315 15203 Z= 0.399 Chirality : 0.047 0.375 1733 Planarity : 0.005 0.039 1077 Dihedral : 32.830 178.678 3289 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 2.40 % Allowed : 18.04 % Favored : 79.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.09 (0.33), residues: 583 helix: 2.13 (0.23), residues: 459 sheet: None (None), residues: 0 loop : -1.55 (0.44), residues: 124 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 78 TYR 0.023 0.002 TYR F 88 PHE 0.014 0.002 PHE E 78 TRP 0.007 0.001 TRP C 86 HIS 0.003 0.001 HIS D 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00512 / 0.23 (10488) covalent geometry : angle 0.71463 / 0.40 (15203) hydrogen bonds : bond 0.06163 / 4.03 ( 672) hydrogen bonds : angle 2.99435 / 2.18 ( 1674) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1166 Ramachandran restraints generated. 583 Oldfield, 0 Emsley, 583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1166 Ramachandran restraints generated. 583 Oldfield, 0 Emsley, 583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 55 time to evaluate : 0.165 Fit side-chains REVERT: B 92 ARG cc_start: 0.7573 (ttp80) cc_final: 0.7311 (ttm-80) REVERT: D 44 LYS cc_start: 0.6004 (mtpp) cc_final: 0.5531 (mmmt) REVERT: E 122 PHE cc_start: 0.8823 (OUTLIER) cc_final: 0.8527 (m-80) REVERT: G 60 LEU cc_start: 0.8328 (OUTLIER) cc_final: 0.8077 (mt) outliers start: 12 outliers final: 9 residues processed: 67 average time/residue: 0.1092 time to fit residues: 9.4639 Evaluate side-chains 64 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 53 time to evaluate : 0.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 112 LEU Chi-restraints excluded: chain D residue 70 VAL Chi-restraints excluded: chain E residue 122 PHE Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain G residue 60 LEU Chi-restraints excluded: chain H residue 50 ILE Chi-restraints excluded: chain H residue 82 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 63 optimal weight: 20.0000 chunk 44 optimal weight: 0.0370 chunk 18 optimal weight: 0.5980 chunk 57 optimal weight: 40.0000 chunk 2 optimal weight: 0.6980 chunk 76 optimal weight: 20.0000 chunk 67 optimal weight: 20.0000 chunk 51 optimal weight: 0.9980 chunk 7 optimal weight: 0.9990 chunk 37 optimal weight: 3.9990 chunk 4 optimal weight: 0.5980 overall best weight: 0.5858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 27 GLN D 27 GLN E 95 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4215 r_free = 0.4215 target = 0.198661 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.143488 restraints weight = 11837.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.139491 restraints weight = 21774.365| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.141576 restraints weight = 16660.479| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.142356 restraints weight = 12063.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.143215 restraints weight = 11369.074| |-----------------------------------------------------------------------------| r_work (final): 0.3512 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7802 moved from start: 0.3809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 10488 Z= 0.144 Angle : 0.621 8.041 15203 Z= 0.362 Chirality : 0.044 0.369 1733 Planarity : 0.004 0.039 1077 Dihedral : 32.721 178.981 3289 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 1.80 % Allowed : 18.44 % Favored : 79.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.71 (0.34), residues: 583 helix: 2.55 (0.23), residues: 459 sheet: None (None), residues: 0 loop : -1.30 (0.46), residues: 124 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG F 78 TYR 0.015 0.002 TYR F 88 PHE 0.014 0.001 PHE E 67 TRP 0.010 0.001 TRP C 86 HIS 0.003 0.001 HIS G 104 Details of bonding type rmsd/Z covalent geometry : bond 0.00246 / 0.14 (10488) covalent geometry : angle 0.62079 / 0.36 (15203) hydrogen bonds : bond 0.04990 / 3.25 ( 672) hydrogen bonds : angle 2.76571 / 2.02 ( 1674) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1166 Ramachandran restraints generated. 583 Oldfield, 0 Emsley, 583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1166 Ramachandran restraints generated. 583 Oldfield, 0 Emsley, 583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 53 time to evaluate : 0.160 Fit side-chains REVERT: D 44 LYS cc_start: 0.6077 (mtpp) cc_final: 0.5530 (mmmt) REVERT: E 122 PHE cc_start: 0.8632 (OUTLIER) cc_final: 0.8328 (m-80) outliers start: 9 outliers final: 8 residues processed: 62 average time/residue: 0.1220 time to fit residues: 9.7211 Evaluate side-chains 61 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 52 time to evaluate : 0.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain C residue 112 LEU Chi-restraints excluded: chain D residue 46 ILE Chi-restraints excluded: chain E residue 122 PHE Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain H residue 50 ILE Chi-restraints excluded: chain H residue 82 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 22 optimal weight: 0.8980 chunk 62 optimal weight: 20.0000 chunk 20 optimal weight: 1.9990 chunk 44 optimal weight: 0.0980 chunk 66 optimal weight: 20.0000 chunk 47 optimal weight: 0.0570 chunk 24 optimal weight: 0.9990 chunk 50 optimal weight: 1.9990 chunk 10 optimal weight: 0.7980 chunk 19 optimal weight: 0.6980 chunk 1 optimal weight: 0.9980 overall best weight: 0.5098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 27 GLN D 27 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4239 r_free = 0.4239 target = 0.201136 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.138979 restraints weight = 11753.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.139058 restraints weight = 22177.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.140412 restraints weight = 20321.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.140852 restraints weight = 14734.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.141679 restraints weight = 14472.123| |-----------------------------------------------------------------------------| r_work (final): 0.3524 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7761 moved from start: 0.3866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 10488 Z= 0.137 Angle : 0.598 8.354 15203 Z= 0.351 Chirality : 0.042 0.369 1733 Planarity : 0.004 0.039 1077 Dihedral : 32.625 179.986 3289 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 1.80 % Allowed : 18.24 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.95 (0.33), residues: 583 helix: 2.80 (0.23), residues: 455 sheet: None (None), residues: 0 loop : -1.37 (0.44), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG F 40 TYR 0.011 0.001 TYR F 88 PHE 0.012 0.001 PHE E 67 TRP 0.009 0.001 TRP C 86 HIS 0.002 0.001 HIS E 59 Details of bonding type rmsd/Z covalent geometry : bond 0.00234 / 0.14 (10488) covalent geometry : angle 0.59843 / 0.35 (15203) hydrogen bonds : bond 0.04727 / 3.07 ( 672) hydrogen bonds : angle 2.65456 / 1.94 ( 1674) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1166 Ramachandran restraints generated. 583 Oldfield, 0 Emsley, 583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1166 Ramachandran restraints generated. 583 Oldfield, 0 Emsley, 583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 55 time to evaluate : 0.176 Fit side-chains revert: symmetry clash REVERT: D 40 ARG cc_start: 0.7870 (ttp-170) cc_final: 0.7608 (ttm170) REVERT: D 44 LYS cc_start: 0.5973 (mtpp) cc_final: 0.5375 (mmmt) REVERT: E 122 PHE cc_start: 0.8680 (OUTLIER) cc_final: 0.8378 (m-80) outliers start: 9 outliers final: 7 residues processed: 64 average time/residue: 0.1334 time to fit residues: 10.7940 Evaluate side-chains 61 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 53 time to evaluate : 0.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain C residue 112 LEU Chi-restraints excluded: chain D residue 46 ILE Chi-restraints excluded: chain E residue 122 PHE Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain H residue 50 ILE Chi-restraints excluded: chain H residue 82 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 14 optimal weight: 0.0980 chunk 4 optimal weight: 0.6980 chunk 17 optimal weight: 0.7980 chunk 52 optimal weight: 0.5980 chunk 43 optimal weight: 0.8980 chunk 24 optimal weight: 0.9980 chunk 25 optimal weight: 0.7980 chunk 75 optimal weight: 20.0000 chunk 61 optimal weight: 20.0000 chunk 0 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 27 GLN D 27 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4233 r_free = 0.4233 target = 0.200677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.141275 restraints weight = 11850.688| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.140417 restraints weight = 22838.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.142010 restraints weight = 19062.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.142898 restraints weight = 13530.977| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.143727 restraints weight = 13075.122| |-----------------------------------------------------------------------------| r_work (final): 0.3593 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7757 moved from start: 0.3916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 10488 Z= 0.138 Angle : 0.597 7.584 15203 Z= 0.350 Chirality : 0.043 0.366 1733 Planarity : 0.004 0.039 1077 Dihedral : 32.593 179.395 3289 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 1.80 % Allowed : 18.24 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.02 (0.33), residues: 583 helix: 2.84 (0.23), residues: 455 sheet: None (None), residues: 0 loop : -1.32 (0.45), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 78 TYR 0.011 0.001 TYR F 88 PHE 0.011 0.001 PHE E 67 TRP 0.009 0.001 TRP C 86 HIS 0.002 0.000 HIS E 115 Details of bonding type rmsd/Z covalent geometry : bond 0.00241 / 0.14 (10488) covalent geometry : angle 0.59657 / 0.35 (15203) hydrogen bonds : bond 0.04703 / 3.07 ( 672) hydrogen bonds : angle 2.64529 / 1.93 ( 1674) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1031.17 seconds wall clock time: 18 minutes 23.80 seconds (1103.80 seconds total)