Starting phenix.real_space_refine on Thu Jul 2 17:19:46 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9k9l_62193/07_2026/9k9l_62193.cif Found real_map, /net/cci-nas-00/data/ceres_data/9k9l_62193/07_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9k9l_62193/07_2026/9k9l_62193.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9k9l_62193/07_2026/9k9l_62193.map" model { file = "/net/cci-nas-00/data/ceres_data/9k9l_62193/07_2026/9k9l_62193.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9k9l_62193/07_2026/9k9l_62193.cif" } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/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: 2.38, per 1000 atoms: 0.24 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: 0.81 Conformation dependent library (CDL) restraints added in 113.5 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: 1.38 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: 1.83 Time building geometry restraints manager: 1.00 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: 13967 1.46 - 2.91: 1143 2.91 - 4.37: 66 4.37 - 5.82: 24 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: 0.540 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: 0.030 Process input model: 10.490 Find NCS groups from input model: 0.120 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: 0.010 Load rotamer database and sin/cos tables:1.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.720 ------------------------------------------------------------------------------- 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= 0.527 Angle : 0.803 7.280 15203 Z= 0.696 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 0.80334 / 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 : 0.269 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: 0.8053 (m-40) REVERT: G 80 ARG cc_start: 0.7452 (mtm-85) cc_final: 0.7045 (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: 0.2170 time to fit residues: 21.5485 Evaluate side-chains 57 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 57 time to evaluate : 0.248 ------------------------------------------------------------------------------- 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: 10.0000 chunk 62 optimal weight: 20.0000 chunk 51 optimal weight: 0.9980 chunk 38 optimal weight: 0.9980 chunk 61 optimal weight: 20.0000 chunk 45 optimal weight: 0.6980 chunk 74 optimal weight: 20.0000 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 = 0.4388 r_free = 0.4388 target = 0.216406 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.153334 restraints weight = 11776.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.151402 restraints weight = 18885.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.153166 restraints weight = 15252.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.153663 restraints weight = 11390.928| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.154466 restraints weight = 11233.555| |-----------------------------------------------------------------------------| r_work (final): 0.3733 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7552 moved from start: 0.1018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10488 Z= 0.165 Angle : 0.624 6.172 15203 Z= 0.378 Chirality : 0.044 0.292 1733 Planarity : 0.005 0.049 1077 Dihedral : 32.118 177.667 3289 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.34 % Favored : 99.66 % Rotamer: Outliers : 1.00 % Allowed : 8.42 % Favored : 90.58 % 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: 2.47 (0.32), residues: 583 helix: 2.34 (0.23), residues: 456 sheet: None (None), residues: 0 loop : -1.07 (0.40), residues: 127 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG H 40 TYR 0.011 0.002 TYR A 110 PHE 0.013 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 / 0.17 (10488) covalent geometry : angle 0.62423 / 0.38 (15203) hydrogen bonds : bond 0.05674 / 3.74 ( 672) hydrogen bonds : angle 3.02480 / 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 63 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 58 time to evaluate : 0.244 Fit side-chains revert: symmetry clash REVERT: B 92 ARG cc_start: 0.7479 (ttp80) cc_final: 0.6923 (ttp-170) REVERT: E 85 ASN cc_start: 0.8217 (m-40) cc_final: 0.8007 (m110) REVERT: G 80 ARG cc_start: 0.7294 (mtm-85) cc_final: 0.7054 (ptp90) REVERT: H 91 LYS cc_start: 0.7915 (tttt) cc_final: 0.7629 (ttmt) REVERT: H 93 GLN cc_start: 0.7744 (tm-30) cc_final: 0.7505 (tm-30) outliers start: 5 outliers final: 2 residues processed: 62 average time/residue: 0.1641 time to fit residues: 12.9008 Evaluate side-chains 56 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 54 time to evaluate : 0.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 43 VAL 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: 0.3980 chunk 13 optimal weight: 0.9980 chunk 40 optimal weight: 4.9990 chunk 74 optimal weight: 20.0000 chunk 18 optimal weight: 0.8980 chunk 49 optimal weight: 3.9990 chunk 64 optimal weight: 20.0000 chunk 36 optimal weight: 0.7980 chunk 32 optimal weight: 0.7980 chunk 45 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 = 0.4400 r_free = 0.4400 target = 0.217224 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.156207 restraints weight = 11754.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.153566 restraints weight = 19617.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.155208 restraints weight = 14983.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.156403 restraints weight = 11326.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.157104 restraints weight = 11032.009| |-----------------------------------------------------------------------------| r_work (final): 0.3679 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7563 moved from start: 0.1447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 10488 Z= 0.154 Angle : 0.587 5.784 15203 Z= 0.359 Chirality : 0.043 0.332 1733 Planarity : 0.004 0.041 1077 Dihedral : 32.237 174.215 3289 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.03 % Favored : 98.97 % Rotamer: Outliers : 2.20 % Allowed : 9.62 % 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: 2.94 (0.33), residues: 583 helix: 2.70 (0.23), residues: 456 sheet: None (None), residues: 0 loop : -1.00 (0.41), residues: 127 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 78 TYR 0.021 0.002 TYR F 72 PHE 0.011 0.001 PHE E 67 TRP 0.021 0.002 TRP C 86 HIS 0.004 0.001 HIS H 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.15 (10488) covalent geometry : angle 0.58719 / 0.36 (15203) hydrogen bonds : bond 0.05151 / 3.38 ( 672) hydrogen bonds : angle 2.80716 / 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 73 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 62 time to evaluate : 0.301 Fit side-chains revert: symmetry clash REVERT: B 84 MET cc_start: 0.7048 (mmt) cc_final: 0.6831 (tpp) REVERT: D 50 ILE cc_start: 0.8450 (OUTLIER) cc_final: 0.8105 (tp) REVERT: F 36 ARG cc_start: 0.7964 (mpp80) cc_final: 0.7692 (mpp80) REVERT: G 80 ARG cc_start: 0.7323 (mtm-85) cc_final: 0.7078 (ptp90) REVERT: H 40 ARG cc_start: 0.8469 (ttm170) cc_final: 0.8263 (ttm170) REVERT: H 91 LYS cc_start: 0.8023 (tttt) cc_final: 0.7727 (ttmt) outliers start: 11 outliers final: 7 residues processed: 70 average time/residue: 0.1726 time to fit residues: 15.3120 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 : 0.311 ------------------------------------------------------------------------------- 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 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=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: 3.9990 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: 9.9990 chunk 68 optimal weight: 30.0000 chunk 53 optimal weight: 0.9990 chunk 79 optimal weight: 40.0000 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4225 r_free = 0.4225 target = 0.197978 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.138519 restraints weight = 12013.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.139329 restraints weight = 29360.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.140841 restraints weight = 19029.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.143076 restraints weight = 13355.836| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.143472 restraints weight = 12130.607| |-----------------------------------------------------------------------------| r_work (final): 0.3573 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7816 moved from start: 0.3064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.077 10488 Z= 0.324 Angle : 0.882 10.882 15203 Z= 0.478 Chirality : 0.055 0.336 1733 Planarity : 0.007 0.060 1077 Dihedral : 32.854 177.187 3289 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 11.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 4.61 % Allowed : 13.23 % 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 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: 1.06 (0.32), residues: 583 helix: 1.34 (0.23), residues: 455 sheet: None (None), residues: 0 loop : -1.54 (0.42), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 67 TYR 0.042 0.004 TYR F 88 PHE 0.019 0.003 PHE E 78 TRP 0.015 0.004 TRP C 86 HIS 0.012 0.002 HIS H 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00753 / 0.32 (10488) covalent geometry : angle 0.88152 / 0.48 (15203) hydrogen bonds : bond 0.08181 / 5.40 ( 672) hydrogen bonds : angle 3.47512 / 2.52 ( 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 96 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 73 time to evaluate : 0.152 Fit side-chains REVERT: B 92 ARG cc_start: 0.7297 (ttp80) cc_final: 0.6941 (ttm170) REVERT: D 50 ILE cc_start: 0.8710 (OUTLIER) cc_final: 0.8257 (tp) REVERT: F 80 THR cc_start: 0.8041 (OUTLIER) cc_final: 0.7840 (t) REVERT: G 60 LEU cc_start: 0.8301 (OUTLIER) cc_final: 0.7990 (mt) REVERT: G 80 ARG cc_start: 0.7164 (mtm-85) cc_final: 0.6799 (ptp90) outliers start: 23 outliers final: 10 residues processed: 93 average time/residue: 0.1412 time to fit residues: 16.5779 Evaluate side-chains 72 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 59 time to evaluate : 0.193 ------------------------------------------------------------------------------- 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 D residue 50 ILE Chi-restraints excluded: chain D residue 70 VAL 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 82 VAL Chi-restraints excluded: chain H residue 43 VAL 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: 0.9990 chunk 43 optimal weight: 0.4980 chunk 5 optimal weight: 0.5980 chunk 23 optimal weight: 0.8980 chunk 9 optimal weight: 0.8980 chunk 58 optimal weight: 20.0000 chunk 0 optimal weight: 0.5980 chunk 3 optimal weight: 0.8980 chunk 75 optimal weight: 20.0000 chunk 10 optimal weight: 0.8980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 27 GLN G 115 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4245 r_free = 0.4245 target = 0.201127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.143084 restraints weight = 11862.543| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.141271 restraints weight = 24868.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.143236 restraints weight = 19266.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.144048 restraints weight = 13344.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.144792 restraints weight = 12638.864| |-----------------------------------------------------------------------------| r_work (final): 0.3581 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7741 moved from start: 0.2959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 10488 Z= 0.154 Angle : 0.631 7.894 15203 Z= 0.371 Chirality : 0.045 0.343 1733 Planarity : 0.004 0.036 1077 Dihedral : 32.678 179.183 3289 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 3.41 % Allowed : 14.83 % Favored : 81.76 % 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: 2.38 (0.33), residues: 583 helix: 2.28 (0.23), residues: 457 sheet: None (None), residues: 0 loop : -1.15 (0.44), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 78 TYR 0.017 0.002 TYR F 88 PHE 0.011 0.001 PHE E 67 TRP 0.011 0.001 TRP C 86 HIS 0.004 0.001 HIS A 115 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.15 (10488) covalent geometry : angle 0.63125 / 0.37 (15203) hydrogen bonds : bond 0.05470 / 3.56 ( 672) hydrogen bonds : angle 2.92650 / 2.12 ( 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 74 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 57 time to evaluate : 0.242 Fit side-chains outliers start: 17 outliers final: 11 residues processed: 71 average time/residue: 0.1573 time to fit residues: 14.2466 Evaluate side-chains 66 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 55 time to evaluate : 0.242 ------------------------------------------------------------------------------- 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 E residue 60 LEU Chi-restraints excluded: chain E residue 61 LEU 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 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: 0.0040 chunk 63 optimal weight: 20.0000 chunk 28 optimal weight: 0.7980 chunk 73 optimal weight: 20.0000 chunk 72 optimal weight: 10.0000 chunk 61 optimal weight: 20.0000 chunk 12 optimal weight: 0.3980 chunk 64 optimal weight: 20.0000 chunk 29 optimal weight: 0.7980 chunk 68 optimal weight: 30.0000 chunk 60 optimal weight: 20.0000 overall best weight: 2.3996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 27 GLN B 75 HIS D 27 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4188 r_free = 0.4188 target = 0.195465 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.137325 restraints weight = 11936.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.139894 restraints weight = 29714.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.140807 restraints weight = 20113.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.142084 restraints weight = 13173.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.142622 restraints weight = 11730.444| |-----------------------------------------------------------------------------| r_work (final): 0.3558 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7796 moved from start: 0.3480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.067 10488 Z= 0.249 Angle : 0.725 8.908 15203 Z= 0.405 Chirality : 0.047 0.345 1733 Planarity : 0.005 0.061 1077 Dihedral : 32.852 179.310 3289 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 10.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 2.81 % Allowed : 17.64 % 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: 1.97 (0.33), residues: 583 helix: 2.02 (0.23), residues: 459 sheet: None (None), residues: 0 loop : -1.47 (0.43), residues: 124 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 78 TYR 0.024 0.002 TYR F 88 PHE 0.016 0.002 PHE A 78 TRP 0.008 0.002 TRP C 86 HIS 0.004 0.001 HIS D 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00567 / 0.25 (10488) covalent geometry : angle 0.72514 / 0.41 (15203) hydrogen bonds : bond 0.06384 / 4.18 ( 672) hydrogen bonds : angle 3.05835 / 2.22 ( 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 72 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 58 time to evaluate : 0.285 Fit side-chains REVERT: B 50 ILE cc_start: 0.8457 (OUTLIER) cc_final: 0.7989 (tp) REVERT: D 44 LYS cc_start: 0.6061 (mtpp) cc_final: 0.5467 (mmmt) outliers start: 14 outliers final: 9 residues processed: 71 average time/residue: 0.1534 time to fit residues: 13.9597 Evaluate side-chains 66 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 56 time to evaluate : 0.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 50 ILE 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 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: 0.7980 chunk 45 optimal weight: 0.5980 chunk 57 optimal weight: 40.0000 chunk 74 optimal weight: 20.0000 chunk 77 optimal weight: 20.0000 chunk 33 optimal weight: 0.9990 chunk 16 optimal weight: 0.9980 chunk 75 optimal weight: 20.0000 chunk 78 optimal weight: 30.0000 chunk 22 optimal weight: 0.7980 chunk 14 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 = 0.4268 r_free = 0.4268 target = 0.203553 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.144621 restraints weight = 11739.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.145347 restraints weight = 25637.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.146947 restraints weight = 18755.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.147851 restraints weight = 13112.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.148574 restraints weight = 12319.693| |-----------------------------------------------------------------------------| r_work (final): 0.3574 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7742 moved from start: 0.3496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 10488 Z= 0.153 Angle : 0.615 9.009 15203 Z= 0.362 Chirality : 0.044 0.340 1733 Planarity : 0.004 0.038 1077 Dihedral : 32.781 179.446 3289 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 2.20 % Allowed : 19.24 % Favored : 78.56 % 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: 2.56 (0.34), residues: 583 helix: 2.44 (0.23), residues: 459 sheet: None (None), residues: 0 loop : -1.33 (0.45), residues: 124 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 78 TYR 0.016 0.002 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 D 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.15 (10488) covalent geometry : angle 0.61515 / 0.36 (15203) hydrogen bonds : bond 0.05174 / 3.37 ( 672) hydrogen bonds : angle 2.80210 / 2.04 ( 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 70 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 59 time to evaluate : 0.242 Fit side-chains REVERT: D 44 LYS cc_start: 0.6071 (mtpp) cc_final: 0.5457 (mmmt) outliers start: 11 outliers final: 7 residues processed: 69 average time/residue: 0.1617 time to fit residues: 14.0938 Evaluate side-chains 63 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 56 time to evaluate : 0.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 112 LEU Chi-restraints excluded: chain D residue 50 ILE Chi-restraints excluded: chain E residue 60 LEU 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: 0.6980 chunk 75 optimal weight: 20.0000 chunk 42 optimal weight: 3.9990 chunk 64 optimal weight: 20.0000 chunk 28 optimal weight: 3.9990 chunk 21 optimal weight: 5.9990 chunk 78 optimal weight: 30.0000 chunk 26 optimal weight: 5.9990 chunk 41 optimal weight: 1.9990 overall best weight: 2.9388 ------------------------------------------------------------------------------- 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 = 0.4183 r_free = 0.4183 target = 0.194915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.136737 restraints weight = 11921.211| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.137725 restraints weight = 28710.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.139283 restraints weight = 18241.322| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.140643 restraints weight = 12847.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.141244 restraints weight = 11754.237| |-----------------------------------------------------------------------------| r_work (final): 0.3512 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 moved from start: 0.3981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.069 10488 Z= 0.276 Angle : 0.746 10.229 15203 Z= 0.413 Chirality : 0.048 0.343 1733 Planarity : 0.005 0.044 1077 Dihedral : 32.989 177.558 3289 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 3.01 % Allowed : 19.04 % Favored : 77.96 % 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: 1.87 (0.33), residues: 583 helix: 1.96 (0.23), residues: 459 sheet: None (None), residues: 0 loop : -1.61 (0.43), residues: 124 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 78 TYR 0.024 0.002 TYR F 88 PHE 0.015 0.002 PHE E 78 TRP 0.008 0.002 TRP C 86 HIS 0.003 0.001 HIS G 104 Details of bonding type rmsd/Z covalent geometry : bond 0.00648 / 0.28 (10488) covalent geometry : angle 0.74627 / 0.41 (15203) hydrogen bonds : bond 0.06471 / 4.24 ( 672) hydrogen bonds : angle 3.06459 / 2.22 ( 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 74 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 59 time to evaluate : 0.269 Fit side-chains REVERT: D 44 LYS cc_start: 0.6026 (mtpp) cc_final: 0.5496 (mmmt) REVERT: G 60 LEU cc_start: 0.8405 (OUTLIER) cc_final: 0.8106 (mt) outliers start: 15 outliers final: 12 residues processed: 74 average time/residue: 0.1350 time to fit residues: 13.1771 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 : 0.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 LEU 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 C residue 112 LEU Chi-restraints excluded: chain D residue 50 ILE Chi-restraints excluded: chain E residue 60 LEU 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: 0.6980 chunk 18 optimal weight: 0.6980 chunk 57 optimal weight: 40.0000 chunk 2 optimal weight: 0.8980 chunk 76 optimal weight: 9.9990 chunk 67 optimal weight: 20.0000 chunk 51 optimal weight: 0.5980 chunk 7 optimal weight: 0.8980 chunk 37 optimal weight: 0.9980 chunk 4 optimal weight: 0.5980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.4215 r_free = 0.4215 target = 0.198734 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.138957 restraints weight = 11812.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.139214 restraints weight = 23393.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.140564 restraints weight = 19035.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.141420 restraints weight = 13489.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.142360 restraints weight = 12206.965| |-----------------------------------------------------------------------------| r_work (final): 0.3520 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7792 moved from start: 0.3956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 10488 Z= 0.151 Angle : 0.614 8.009 15203 Z= 0.361 Chirality : 0.044 0.336 1733 Planarity : 0.004 0.044 1077 Dihedral : 32.862 178.320 3289 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 1.20 % Allowed : 20.84 % Favored : 77.96 % 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: 2.56 (0.34), residues: 583 helix: 2.45 (0.23), residues: 459 sheet: None (None), residues: 0 loop : -1.34 (0.45), residues: 124 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 78 TYR 0.016 0.002 TYR F 88 PHE 0.012 0.001 PHE E 67 TRP 0.011 0.001 TRP C 86 HIS 0.003 0.001 HIS G 104 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.15 (10488) covalent geometry : angle 0.61391 / 0.36 (15203) hydrogen bonds : bond 0.05005 / 3.27 ( 672) hydrogen bonds : angle 2.77092 / 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: 6 poor density : 56 time to evaluate : 0.248 Fit side-chains REVERT: D 44 LYS cc_start: 0.5978 (mtpp) cc_final: 0.5449 (mmmt) outliers start: 6 outliers final: 6 residues processed: 62 average time/residue: 0.1598 time to fit residues: 12.6290 Evaluate side-chains 64 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 58 time to evaluate : 0.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain C residue 112 LEU Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain H residue 50 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 22 optimal weight: 2.9990 chunk 62 optimal weight: 20.0000 chunk 20 optimal weight: 0.6980 chunk 44 optimal weight: 1.9990 chunk 66 optimal weight: 20.0000 chunk 47 optimal weight: 0.9990 chunk 24 optimal weight: 0.9980 chunk 50 optimal weight: 1.9990 chunk 10 optimal weight: 0.6980 chunk 19 optimal weight: 0.9990 chunk 1 optimal weight: 0.7980 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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 = 0.4212 r_free = 0.4212 target = 0.198586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.138265 restraints weight = 11711.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.137439 restraints weight = 22403.300| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.139085 restraints weight = 18838.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.140231 restraints weight = 13625.004| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.140983 restraints weight = 13215.283| |-----------------------------------------------------------------------------| r_work (final): 0.3505 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7826 moved from start: 0.4030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10488 Z= 0.152 Angle : 0.610 8.261 15203 Z= 0.356 Chirality : 0.043 0.340 1733 Planarity : 0.004 0.041 1077 Dihedral : 32.817 178.951 3289 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 2.00 % Allowed : 19.84 % Favored : 78.16 % 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: 2.78 (0.33), residues: 583 helix: 2.58 (0.23), residues: 459 sheet: None (None), residues: 0 loop : -1.16 (0.46), residues: 124 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG F 78 TYR 0.013 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 0.00288 / 0.15 (10488) covalent geometry : angle 0.60953 / 0.36 (15203) hydrogen bonds : bond 0.04977 / 3.24 ( 672) hydrogen bonds : angle 2.72246 / 1.98 ( 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 68 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 58 time to evaluate : 0.322 Fit side-chains revert: symmetry clash REVERT: D 44 LYS cc_start: 0.5947 (mtpp) cc_final: 0.5446 (mmmt) outliers start: 10 outliers final: 8 residues processed: 68 average time/residue: 0.1795 time to fit residues: 15.1132 Evaluate side-chains 64 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 56 time to evaluate : 0.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain C residue 112 LEU Chi-restraints excluded: chain D residue 50 ILE Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain H residue 50 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 14 optimal weight: 2.9990 chunk 4 optimal weight: 0.6980 chunk 17 optimal weight: 0.8980 chunk 52 optimal weight: 0.8980 chunk 43 optimal weight: 0.5980 chunk 24 optimal weight: 0.9980 chunk 25 optimal weight: 0.8980 chunk 75 optimal weight: 20.0000 chunk 61 optimal weight: 20.0000 chunk 0 optimal weight: 2.9990 chunk 48 optimal weight: 0.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 = 0.4268 r_free = 0.4268 target = 0.204379 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.145422 restraints weight = 11767.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.148020 restraints weight = 25623.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.148661 restraints weight = 19178.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.149052 restraints weight = 13339.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.149726 restraints weight = 12369.968| |-----------------------------------------------------------------------------| r_work (final): 0.3608 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7738 moved from start: 0.4126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10488 Z= 0.145 Angle : 0.592 7.777 15203 Z= 0.350 Chirality : 0.042 0.334 1733 Planarity : 0.004 0.039 1077 Dihedral : 32.763 178.500 3289 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Rotamer: Outliers : 1.60 % Allowed : 20.84 % Favored : 77.56 % 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: 2.89 (0.33), residues: 583 helix: 2.66 (0.23), residues: 459 sheet: None (None), residues: 0 loop : -1.15 (0.46), residues: 124 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 78 TYR 0.013 0.001 TYR F 88 PHE 0.011 0.001 PHE E 67 TRP 0.009 0.001 TRP C 86 HIS 0.002 0.001 HIS G 59 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.14 (10488) covalent geometry : angle 0.59214 / 0.35 (15203) hydrogen bonds : bond 0.04766 / 3.12 ( 672) hydrogen bonds : angle 2.67351 / 1.94 ( 1674) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1344.39 seconds wall clock time: 24 minutes 3.83 seconds (1443.83 seconds total)