Starting phenix.real_space_refine on Fri Jul 3 01:51:01 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9k42_62040/07_2026/9k42_62040.cif Found real_map, /net/cci-nas-00/data/ceres_data/9k42_62040/07_2026/9k42_62040.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.14 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9k42_62040/07_2026/9k42_62040.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9k42_62040/07_2026/9k42_62040.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9k42_62040/07_2026/9k42_62040.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9k42_62040/07_2026/9k42_62040.map" } resolution = 3.14 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= 0.001 sd= 0.043 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 289 5.49 5 S 12 5.16 5 C 6552 2.51 5 N 2191 2.21 5 O 2780 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 25 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: 11824 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 783 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 3, 'TRANS': 92} Chain: "B" Number of atoms: 644 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 644 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 1, 'TRANS': 78} Chain: "C" Number of atoms: 783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 783 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 5, 'TRANS': 98} Chain: "D" Number of atoms: 731 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 731 Classifications: {'peptide': 93} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 89} Chain: "E" Number of atoms: 783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 783 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 3, 'TRANS': 92} Chain: "F" Number of atoms: 644 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 644 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 1, 'TRANS': 78} Chain: "G" Number of atoms: 783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 783 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 5, 'TRANS': 98} Chain: "H" Number of atoms: 731 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 731 Classifications: {'peptide': 93} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 89} Chain: "I" Number of atoms: 2957 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 2957 Classifications: {'DNA': 145} Link IDs: {'rna3p': 144} Chain: "J" Number of atoms: 2985 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 2985 Classifications: {'DNA': 145} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 144} Time building chain proxies: 2.98, per 1000 atoms: 0.25 Number of scatterers: 11824 At special positions: 0 Unit cell: (88.976, 120.064, 114.704, 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 12 16.00 P 289 15.00 O 2780 8.00 N 2191 7.00 C 6552 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: 0.85 Conformation dependent library (CDL) restraints added in 152.6 milliseconds 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1396 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 10 sheets defined 75.1% alpha, 2.7% beta 126 base pairs and 278 stacking pairs defined. Time for finding SS restraints: 2.07 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 removed outlier: 3.596A pdb=" N LYS A 56 " --> pdb=" O ARG A 52 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 77 removed outlier: 3.859A pdb=" N ASP A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 132 Processing helix chain 'B' and resid 25 through 29 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 93 removed outlier: 3.571A pdb=" N GLN B 93 " --> pdb=" O ALA B 89 " (cutoff:3.500A) Processing helix chain 'C' and resid 17 through 23 Processing helix chain 'C' and resid 27 through 38 Processing helix chain 'C' and resid 46 through 75 removed outlier: 4.584A pdb=" N VAL C 50 " --> pdb=" O ALA C 46 " (cutoff:3.500A) Processing helix chain 'C' and resid 80 through 91 Processing helix chain 'C' and resid 91 through 98 Processing helix chain 'C' and resid 113 through 117 Processing helix chain 'D' and resid 60 through 72 Processing helix chain 'D' and resid 78 through 108 Processing helix chain 'D' and resid 113 through 125 Processing helix chain 'D' and resid 126 through 146 Processing helix chain 'E' and resid 44 through 57 removed outlier: 3.560A pdb=" N LYS E 56 " --> pdb=" O ARG E 52 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 77 removed outlier: 3.882A pdb=" N ASP E 77 " --> pdb=" O GLU E 73 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 132 Processing helix chain 'F' and resid 25 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 93 removed outlier: 3.501A pdb=" N VAL F 86 " --> pdb=" O THR F 82 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLN F 93 " --> pdb=" O ALA F 89 " (cutoff:3.500A) Processing helix chain 'G' and resid 17 through 23 Processing helix chain 'G' and resid 27 through 38 Processing helix chain 'G' and resid 47 through 74 Processing helix chain 'G' and resid 80 through 91 Processing helix chain 'G' and resid 91 through 98 Processing helix chain 'G' and resid 113 through 117 Processing helix chain 'H' and resid 60 through 72 Processing helix chain 'H' and resid 78 through 107 Processing helix chain 'H' and resid 113 through 125 Processing helix chain 'H' and resid 126 through 147 Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 7.059A pdb=" N ARG A 83 " --> 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 118 through 119 Processing sheet with id=AA3, first strand: chain 'B' and resid 97 through 98 Processing sheet with id=AA4, first strand: chain 'C' and resid 43 through 44 removed outlier: 7.384A pdb=" N ARG C 43 " --> pdb=" O ILE D 112 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 78 through 79 Processing sheet with id=AA6, first strand: chain 'C' and resid 102 through 103 removed outlier: 6.894A pdb=" N THR C 102 " --> pdb=" O TYR F 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84 removed outlier: 6.840A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA9, first strand: chain 'G' and resid 43 through 44 removed outlier: 7.258A pdb=" N ARG G 43 " --> pdb=" O ILE H 112 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'G' and resid 78 through 79 417 hydrogen bonds defined for protein. 1227 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 320 hydrogen bonds 640 hydrogen bond angles 0 basepair planarities 126 basepair parallelities 278 stacking parallelities Total time for adding SS restraints: 2.08 Time building geometry restraints manager: 1.15 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2717 1.34 - 1.45: 3756 1.45 - 1.57: 5557 1.57 - 1.69: 577 1.69 - 1.81: 22 Bond restraints: 12629 Sorted by residual: bond pdb=" O5' DA I 50 " pdb=" C5' DA I 50 " ideal model delta sigma weight residual 1.418 1.445 -0.027 2.50e-02 1.60e+03 1.21e+00 bond pdb=" C2' DT I 38 " pdb=" C1' DT I 38 " ideal model delta sigma weight residual 1.518 1.507 0.011 1.00e-02 1.00e+04 1.17e+00 bond pdb=" C2' DA I -67 " pdb=" C1' DA I -67 " ideal model delta sigma weight residual 1.518 1.508 0.010 1.00e-02 1.00e+04 1.07e+00 bond pdb=" O5' DT I 15 " pdb=" C5' DT I 15 " ideal model delta sigma weight residual 1.418 1.443 -0.025 2.50e-02 1.60e+03 9.93e-01 bond pdb=" O5' DT I 55 " pdb=" C5' DT I 55 " ideal model delta sigma weight residual 1.418 1.443 -0.025 2.50e-02 1.60e+03 9.89e-01 ... (remaining 12624 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.92: 17779 1.92 - 3.84: 484 3.84 - 5.76: 32 5.76 - 7.68: 6 7.68 - 9.60: 2 Bond angle restraints: 18303 Sorted by residual: angle pdb=" N ASP B 24 " pdb=" CA ASP B 24 " pdb=" C ASP B 24 " ideal model delta sigma weight residual 111.17 116.66 -5.49 1.41e+00 5.03e-01 1.52e+01 angle pdb=" C3' DG I 54 " pdb=" C2' DG I 54 " pdb=" C1' DG I 54 " ideal model delta sigma weight residual 102.50 97.91 4.59 1.20e+00 6.94e-01 1.47e+01 angle pdb=" N ASP F 24 " pdb=" CA ASP F 24 " pdb=" C ASP F 24 " ideal model delta sigma weight residual 111.17 116.55 -5.38 1.41e+00 5.03e-01 1.46e+01 angle pdb=" N GLY H 127 " pdb=" CA GLY H 127 " pdb=" C GLY H 127 " ideal model delta sigma weight residual 111.02 118.08 -7.06 1.86e+00 2.89e-01 1.44e+01 angle pdb=" N GLY D 127 " pdb=" CA GLY D 127 " pdb=" C GLY D 127 " ideal model delta sigma weight residual 111.02 118.02 -7.00 1.86e+00 2.89e-01 1.42e+01 ... (remaining 18298 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.09: 3992 18.09 - 36.18: 997 36.18 - 54.26: 1393 54.26 - 72.35: 430 72.35 - 90.44: 27 Dihedral angle restraints: 6839 sinusoidal: 4681 harmonic: 2158 Sorted by residual: dihedral pdb=" CA ASN B 64 " pdb=" CB ASN B 64 " pdb=" CG ASN B 64 " pdb=" OD1 ASN B 64 " ideal model delta sinusoidal sigma weight residual 120.00 -165.78 -74.22 2 2.00e+01 2.50e-03 1.11e+01 dihedral pdb=" CB GLU D 99 " pdb=" CG GLU D 99 " pdb=" CD GLU D 99 " pdb=" OE1 GLU D 99 " ideal model delta sinusoidal sigma weight residual 0.00 -90.44 90.44 1 3.00e+01 1.11e-03 1.07e+01 dihedral pdb=" CB GLU C 65 " pdb=" CG GLU C 65 " pdb=" CD GLU C 65 " pdb=" OE1 GLU C 65 " ideal model delta sinusoidal sigma weight residual 0.00 89.99 -89.99 1 3.00e+01 1.11e-03 1.07e+01 ... (remaining 6836 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 1401 0.043 - 0.086: 562 0.086 - 0.129: 114 0.129 - 0.173: 8 0.173 - 0.216: 4 Chirality restraints: 2089 Sorted by residual: chirality pdb=" C3' DG I 54 " pdb=" C4' DG I 54 " pdb=" O3' DG I 54 " pdb=" C2' DG I 54 " both_signs ideal model delta sigma weight residual False -2.73 -2.95 0.22 2.00e-01 2.50e+01 1.16e+00 chirality pdb=" CA ASP B 24 " pdb=" N ASP B 24 " pdb=" C ASP B 24 " pdb=" CB ASP B 24 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.14e+00 chirality pdb=" CA ASP F 24 " pdb=" N ASP F 24 " pdb=" C ASP F 24 " pdb=" CB ASP F 24 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.14e+00 ... (remaining 2086 not shown) Planarity restraints: 1310 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG A 42 " -0.036 5.00e-02 4.00e+02 5.44e-02 4.73e+00 pdb=" N PRO A 43 " 0.094 5.00e-02 4.00e+02 pdb=" CA PRO A 43 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 43 " -0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG E 42 " 0.035 5.00e-02 4.00e+02 5.34e-02 4.56e+00 pdb=" N PRO E 43 " -0.092 5.00e-02 4.00e+02 pdb=" CA PRO E 43 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO E 43 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU D 125 " 0.031 5.00e-02 4.00e+02 4.62e-02 3.41e+00 pdb=" N PRO D 126 " -0.080 5.00e-02 4.00e+02 pdb=" CA PRO D 126 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO D 126 " 0.026 5.00e-02 4.00e+02 ... (remaining 1307 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 157 2.62 - 3.19: 8833 3.19 - 3.76: 21959 3.76 - 4.33: 31580 4.33 - 4.90: 43083 Nonbonded interactions: 105612 Sorted by model distance: nonbonded pdb=" C2' DG I 11 " pdb=" O5' DT I 12 " model vdw 2.050 3.440 nonbonded pdb=" OG1 THR D 59 " pdb=" OD1 ASN D 86 " model vdw 2.273 3.040 nonbonded pdb=" O THR D 142 " pdb=" OG SER D 146 " model vdw 2.277 3.040 nonbonded pdb=" OE1 GLU H 94 " pdb=" NE2 GLN H 98 " model vdw 2.282 3.120 nonbonded pdb=" NH1 ARG F 92 " pdb=" OE1 GLU H 99 " model vdw 2.289 3.120 ... (remaining 105607 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 'E' } ncs_group { reference = chain 'B' selection = chain 'F' } ncs_group { reference = chain 'C' selection = chain 'G' } ncs_group { reference = chain 'D' 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.460 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.010 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.140 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 12.890 Find NCS groups from input model: 0.100 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:1.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7821 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.027 12629 Z= 0.268 Angle : 0.727 9.601 18303 Z= 0.523 Chirality : 0.045 0.216 2089 Planarity : 0.005 0.054 1310 Dihedral : 31.947 90.437 5443 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 0.49 % Allowed : 13.27 % Favored : 86.25 % 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: 2.37 (0.30), residues: 730 helix: 2.17 (0.22), residues: 540 sheet: None (None), residues: 0 loop : -0.15 (0.39), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 30 TYR 0.018 0.002 TYR B 98 PHE 0.007 0.001 PHE E 67 HIS 0.004 0.001 HIS H 132 Details of bonding type rmsd/Z covalent geometry : bond 0.00484 / 0.27 (12629) covalent geometry : angle 0.72705 / 0.52 (18303) hydrogen bonds : bond 0.15768 / 10.96 ( 737) hydrogen bonds : angle 9.50804 / 6.94 ( 1867) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 200 time to evaluate : 0.291 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 88 TYR cc_start: 0.8169 (m-10) cc_final: 0.7154 (m-80) REVERT: F 88 TYR cc_start: 0.8177 (m-10) cc_final: 0.7359 (m-80) REVERT: H 74 ASP cc_start: 0.7813 (p0) cc_final: 0.7497 (p0) outliers start: 3 outliers final: 2 residues processed: 202 average time/residue: 0.1161 time to fit residues: 31.6166 Evaluate side-chains 155 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 153 time to evaluate : 0.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain F residue 23 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 49 optimal weight: 3.9990 chunk 97 optimal weight: 20.0000 chunk 53 optimal weight: 10.0000 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 0.7980 chunk 65 optimal weight: 6.9990 chunk 62 optimal weight: 6.9990 chunk 51 optimal weight: 2.9990 chunk 38 optimal weight: 3.9990 chunk 61 optimal weight: 7.9990 chunk 45 optimal weight: 0.9980 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 39 HIS B 64 ASN ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 74 ASN C 85 GLN C 105 ASN D 56 ASN E 39 HIS E 108 ASN E 113 HIS G 25 GLN G 85 GLN H 56 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.077413 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.054247 restraints weight = 54099.986| |-----------------------------------------------------------------------------| r_work (start): 0.3039 rms_B_bonded: 2.89 r_work (final): 0.3039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8417 moved from start: 0.2112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 12629 Z= 0.213 Angle : 0.860 9.657 18303 Z= 0.454 Chirality : 0.058 0.267 2089 Planarity : 0.006 0.060 1310 Dihedral : 34.683 90.303 3984 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 3.88 % Allowed : 17.48 % Favored : 78.64 % 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: 2.54 (0.30), residues: 730 helix: 2.32 (0.21), residues: 548 sheet: None (None), residues: 0 loop : -0.30 (0.40), residues: 182 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 43 TYR 0.032 0.003 TYR D 106 PHE 0.009 0.001 PHE E 67 HIS 0.008 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00408 / 0.21 (12629) covalent geometry : angle 0.85966 / 0.45 (18303) hydrogen bonds : bond 0.05777 / 4.00 ( 737) hydrogen bonds : angle 3.47334 / 2.52 ( 1867) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 170 time to evaluate : 0.282 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 THR cc_start: 0.9537 (OUTLIER) cc_final: 0.9290 (t) REVERT: C 40 TYR cc_start: 0.9252 (m-80) cc_final: 0.9031 (m-80) REVERT: C 74 ASN cc_start: 0.8701 (OUTLIER) cc_final: 0.8373 (t0) REVERT: C 91 ASP cc_start: 0.7852 (t70) cc_final: 0.7633 (t70) REVERT: D 82 MET cc_start: 0.9201 (tpp) cc_final: 0.8977 (tpp) REVERT: D 91 ASP cc_start: 0.9046 (t0) cc_final: 0.8770 (t0) REVERT: D 98 GLN cc_start: 0.9007 (mm-40) cc_final: 0.8690 (mm-40) REVERT: E 42 ARG cc_start: 0.8085 (mtp180) cc_final: 0.7773 (ttm-80) REVERT: E 58 THR cc_start: 0.9516 (OUTLIER) cc_final: 0.9238 (t) REVERT: E 60 LEU cc_start: 0.9216 (mt) cc_final: 0.8986 (mt) REVERT: E 97 GLU cc_start: 0.8053 (mt-10) cc_final: 0.7705 (mt-10) REVERT: F 88 TYR cc_start: 0.9343 (m-10) cc_final: 0.8511 (m-80) REVERT: G 65 GLU cc_start: 0.8451 (tm-30) cc_final: 0.8178 (tm-30) REVERT: G 93 GLU cc_start: 0.8612 (mm-30) cc_final: 0.8221 (mm-30) REVERT: H 74 ASP cc_start: 0.8987 (p0) cc_final: 0.8625 (p0) REVERT: H 91 ASP cc_start: 0.8925 (t0) cc_final: 0.8651 (t0) REVERT: H 94 GLU cc_start: 0.8861 (mm-30) cc_final: 0.8463 (mm-30) REVERT: H 98 GLN cc_start: 0.9128 (mm-40) cc_final: 0.8699 (mm-40) REVERT: H 106 TYR cc_start: 0.8361 (m-10) cc_final: 0.7920 (m-10) REVERT: H 116 GLU cc_start: 0.8311 (mp0) cc_final: 0.7978 (mp0) outliers start: 24 outliers final: 12 residues processed: 185 average time/residue: 0.1068 time to fit residues: 26.8851 Evaluate side-chains 173 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 158 time to evaluate : 0.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain C residue 74 ASN Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain D residue 113 THR Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain F residue 22 LEU Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 57 GLU Chi-restraints excluded: chain G residue 108 VAL Chi-restraints excluded: chain H residue 62 ILE Chi-restraints excluded: chain H residue 111 THR Chi-restraints excluded: chain H residue 136 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 67 optimal weight: 7.9990 chunk 15 optimal weight: 0.9990 chunk 9 optimal weight: 4.9990 chunk 92 optimal weight: 10.0000 chunk 56 optimal weight: 1.9990 chunk 54 optimal weight: 0.9990 chunk 88 optimal weight: 20.0000 chunk 95 optimal weight: 10.0000 chunk 48 optimal weight: 0.7980 chunk 24 optimal weight: 4.9990 chunk 17 optimal weight: 9.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.075626 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.052957 restraints weight = 53838.304| |-----------------------------------------------------------------------------| r_work (start): 0.3002 rms_B_bonded: 2.73 r_work (final): 0.3002 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8455 moved from start: 0.2616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 12629 Z= 0.166 Angle : 0.656 8.728 18303 Z= 0.376 Chirality : 0.048 0.242 2089 Planarity : 0.005 0.054 1310 Dihedral : 34.363 99.245 3979 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 2.43 % Allowed : 17.96 % Favored : 79.61 % 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 (0.30), residues: 730 helix: 2.51 (0.21), residues: 548 sheet: None (None), residues: 0 loop : -0.25 (0.42), residues: 182 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 30 TYR 0.013 0.002 TYR C 58 PHE 0.011 0.001 PHE A 67 HIS 0.003 0.001 HIS D 72 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.17 (12629) covalent geometry : angle 0.65589 / 0.38 (18303) hydrogen bonds : bond 0.04811 / 3.37 ( 737) hydrogen bonds : angle 3.31422 / 2.41 ( 1867) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 172 time to evaluate : 0.290 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 GLN cc_start: 0.8906 (tm-30) cc_final: 0.8443 (tm-30) REVERT: C 40 TYR cc_start: 0.9231 (m-80) cc_final: 0.8515 (m-80) REVERT: C 92 GLU cc_start: 0.9024 (tp30) cc_final: 0.8124 (tp30) REVERT: C 96 LYS cc_start: 0.9035 (mmmt) cc_final: 0.8275 (mmmt) REVERT: D 91 ASP cc_start: 0.9045 (t0) cc_final: 0.8681 (t0) REVERT: D 94 GLU cc_start: 0.8850 (mm-30) cc_final: 0.8582 (tp30) REVERT: D 116 GLU cc_start: 0.8561 (mp0) cc_final: 0.8118 (mp0) REVERT: E 42 ARG cc_start: 0.8129 (mtp180) cc_final: 0.7702 (ttm-80) REVERT: E 97 GLU cc_start: 0.8059 (mt-10) cc_final: 0.7693 (mt-10) REVERT: F 88 TYR cc_start: 0.9233 (m-10) cc_final: 0.8997 (m-80) REVERT: G 91 ASP cc_start: 0.8616 (t0) cc_final: 0.8306 (t70) REVERT: G 93 GLU cc_start: 0.8731 (mm-30) cc_final: 0.8439 (mm-30) REVERT: H 58 GLU cc_start: 0.7833 (mm-30) cc_final: 0.7608 (mm-30) REVERT: H 74 ASP cc_start: 0.8965 (p0) cc_final: 0.8574 (p0) REVERT: H 91 ASP cc_start: 0.8996 (t0) cc_final: 0.8614 (t0) REVERT: H 94 GLU cc_start: 0.8892 (mm-30) cc_final: 0.8544 (mm-30) REVERT: H 98 GLN cc_start: 0.9192 (mm-40) cc_final: 0.8989 (mm-40) REVERT: H 116 GLU cc_start: 0.8541 (mp0) cc_final: 0.8141 (mp0) REVERT: H 146 SER cc_start: 0.9216 (m) cc_final: 0.8889 (p) outliers start: 15 outliers final: 9 residues processed: 180 average time/residue: 0.1168 time to fit residues: 28.7836 Evaluate side-chains 168 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 159 time to evaluate : 0.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 74 GLU Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain D residue 62 ILE Chi-restraints excluded: chain D residue 113 THR Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 57 GLU Chi-restraints excluded: chain H residue 62 ILE Chi-restraints excluded: chain H residue 136 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 33 optimal weight: 2.9990 chunk 94 optimal weight: 10.0000 chunk 3 optimal weight: 1.9990 chunk 38 optimal weight: 0.0870 chunk 86 optimal weight: 40.0000 chunk 82 optimal weight: 20.0000 chunk 67 optimal weight: 0.8980 chunk 95 optimal weight: 10.0000 chunk 20 optimal weight: 1.9990 chunk 85 optimal weight: 40.0000 chunk 35 optimal weight: 0.9990 overall best weight: 1.1964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 107 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.075614 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.052255 restraints weight = 53936.253| |-----------------------------------------------------------------------------| r_work (start): 0.2993 rms_B_bonded: 2.79 r_work (final): 0.2993 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8475 moved from start: 0.2956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 12629 Z= 0.141 Angle : 0.620 10.899 18303 Z= 0.356 Chirality : 0.045 0.228 2089 Planarity : 0.004 0.048 1310 Dihedral : 34.036 98.094 3979 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 10.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 4.05 % Allowed : 17.64 % Favored : 78.32 % 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 (0.30), residues: 730 helix: 2.58 (0.21), residues: 548 sheet: None (None), residues: 0 loop : -0.21 (0.43), residues: 182 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 105 TYR 0.014 0.002 TYR C 58 PHE 0.011 0.001 PHE E 67 HIS 0.003 0.001 HIS D 72 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.14 (12629) covalent geometry : angle 0.62032 / 0.36 (18303) hydrogen bonds : bond 0.04269 / 2.98 ( 737) hydrogen bonds : angle 3.15079 / 2.28 ( 1867) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 172 time to evaluate : 0.233 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 22 LEU cc_start: 0.7259 (OUTLIER) cc_final: 0.6583 (mt) REVERT: B 88 TYR cc_start: 0.9300 (m-80) cc_final: 0.8980 (m-80) REVERT: C 40 TYR cc_start: 0.9313 (m-80) cc_final: 0.8861 (m-80) REVERT: C 91 ASP cc_start: 0.7972 (t70) cc_final: 0.7631 (t0) REVERT: C 92 GLU cc_start: 0.9026 (tp30) cc_final: 0.8138 (tp30) REVERT: C 96 LYS cc_start: 0.9048 (mmmt) cc_final: 0.8346 (mmmt) REVERT: D 91 ASP cc_start: 0.9062 (t0) cc_final: 0.8698 (t0) REVERT: D 94 GLU cc_start: 0.8920 (mm-30) cc_final: 0.7963 (tp30) REVERT: D 98 GLN cc_start: 0.9188 (mm-40) cc_final: 0.8771 (mm-40) REVERT: D 116 GLU cc_start: 0.8610 (mp0) cc_final: 0.8158 (mp0) REVERT: E 42 ARG cc_start: 0.8033 (mtp180) cc_final: 0.7645 (ttm-80) REVERT: F 88 TYR cc_start: 0.9239 (m-10) cc_final: 0.9013 (m-80) REVERT: G 51 TYR cc_start: 0.9243 (t80) cc_final: 0.8958 (t80) REVERT: G 85 GLN cc_start: 0.8896 (OUTLIER) cc_final: 0.8464 (tm-30) REVERT: G 91 ASP cc_start: 0.8662 (t0) cc_final: 0.8415 (t70) REVERT: G 93 GLU cc_start: 0.8752 (mm-30) cc_final: 0.8483 (mm-30) REVERT: H 58 GLU cc_start: 0.7880 (mm-30) cc_final: 0.7645 (mm-30) REVERT: H 74 ASP cc_start: 0.8979 (p0) cc_final: 0.8605 (p0) REVERT: H 82 MET cc_start: 0.9244 (tpp) cc_final: 0.8988 (tpp) REVERT: H 91 ASP cc_start: 0.9007 (t0) cc_final: 0.8609 (t0) REVERT: H 94 GLU cc_start: 0.8928 (mm-30) cc_final: 0.8214 (tp30) REVERT: H 98 GLN cc_start: 0.9172 (mm-40) cc_final: 0.8681 (mm110) REVERT: H 116 GLU cc_start: 0.8558 (mp0) cc_final: 0.8153 (mp0) REVERT: H 146 SER cc_start: 0.9159 (m) cc_final: 0.8857 (p) outliers start: 25 outliers final: 13 residues processed: 186 average time/residue: 0.1055 time to fit residues: 27.2807 Evaluate side-chains 179 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 164 time to evaluate : 0.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain B residue 44 LYS Chi-restraints excluded: chain B residue 74 GLU Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain D residue 62 ILE Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain F residue 22 LEU Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 44 LYS Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 85 GLN Chi-restraints excluded: chain H residue 57 VAL Chi-restraints excluded: chain H residue 62 ILE Chi-restraints excluded: chain H residue 136 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 91 optimal weight: 20.0000 chunk 49 optimal weight: 0.6980 chunk 48 optimal weight: 0.7980 chunk 28 optimal weight: 0.9990 chunk 12 optimal weight: 4.9990 chunk 27 optimal weight: 2.9990 chunk 2 optimal weight: 5.9990 chunk 94 optimal weight: 9.9990 chunk 90 optimal weight: 10.0000 chunk 35 optimal weight: 0.7980 chunk 62 optimal weight: 0.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 55 GLN A 93 GLN E 93 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.075542 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.052428 restraints weight = 53856.086| |-----------------------------------------------------------------------------| r_work (start): 0.2999 rms_B_bonded: 2.74 r_work (final): 0.2999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8472 moved from start: 0.3288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 12629 Z= 0.127 Angle : 0.599 11.557 18303 Z= 0.347 Chirality : 0.044 0.196 2089 Planarity : 0.005 0.067 1310 Dihedral : 33.769 98.263 3979 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 10.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 3.72 % Allowed : 18.61 % Favored : 77.67 % 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: 2.96 (0.31), residues: 730 helix: 2.64 (0.22), residues: 550 sheet: None (None), residues: 0 loop : -0.25 (0.44), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 89 TYR 0.020 0.002 TYR B 88 PHE 0.013 0.001 PHE A 67 HIS 0.002 0.001 HIS D 72 Details of bonding type rmsd/Z covalent geometry : bond 0.00225 / 0.13 (12629) covalent geometry : angle 0.59871 / 0.35 (18303) hydrogen bonds : bond 0.03929 / 2.75 ( 737) hydrogen bonds : angle 3.09912 / 2.23 ( 1867) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 179 time to evaluate : 0.215 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 22 LEU cc_start: 0.7299 (OUTLIER) cc_final: 0.7006 (mt) REVERT: B 96 THR cc_start: 0.9382 (m) cc_final: 0.8945 (p) REVERT: C 40 TYR cc_start: 0.9285 (m-80) cc_final: 0.8819 (m-80) REVERT: C 92 GLU cc_start: 0.9055 (tp30) cc_final: 0.7991 (tp30) REVERT: C 96 LYS cc_start: 0.9011 (mmmt) cc_final: 0.8314 (mmmt) REVERT: D 91 ASP cc_start: 0.9076 (t0) cc_final: 0.8706 (t0) REVERT: D 94 GLU cc_start: 0.8946 (mm-30) cc_final: 0.7909 (tp30) REVERT: D 98 GLN cc_start: 0.9139 (mm-40) cc_final: 0.8700 (mm-40) REVERT: D 116 GLU cc_start: 0.8617 (mp0) cc_final: 0.8137 (mp0) REVERT: E 42 ARG cc_start: 0.8078 (mtp180) cc_final: 0.7550 (ttm-80) REVERT: G 51 TYR cc_start: 0.9207 (t80) cc_final: 0.8861 (t80) REVERT: G 91 ASP cc_start: 0.8754 (t0) cc_final: 0.8396 (t0) REVERT: G 93 GLU cc_start: 0.8811 (mm-30) cc_final: 0.8453 (mm-30) REVERT: H 58 GLU cc_start: 0.7855 (mm-30) cc_final: 0.7605 (mm-30) REVERT: H 74 ASP cc_start: 0.8979 (p0) cc_final: 0.8620 (p0) REVERT: H 91 ASP cc_start: 0.9034 (t0) cc_final: 0.8635 (t0) REVERT: H 94 GLU cc_start: 0.8934 (mm-30) cc_final: 0.8264 (tp30) REVERT: H 98 GLN cc_start: 0.9197 (mm-40) cc_final: 0.8742 (mm-40) REVERT: H 116 GLU cc_start: 0.8553 (mp0) cc_final: 0.8134 (mp0) REVERT: H 146 SER cc_start: 0.9177 (m) cc_final: 0.8868 (p) outliers start: 23 outliers final: 14 residues processed: 193 average time/residue: 0.1134 time to fit residues: 29.9464 Evaluate side-chains 183 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 168 time to evaluate : 0.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain B residue 23 ARG Chi-restraints excluded: chain B residue 44 LYS Chi-restraints excluded: chain B residue 74 GLU Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain D residue 62 ILE Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain F residue 22 LEU Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 44 LYS Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain H residue 62 ILE Chi-restraints excluded: chain H residue 136 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 76 optimal weight: 20.0000 chunk 66 optimal weight: 3.9990 chunk 27 optimal weight: 2.9990 chunk 92 optimal weight: 10.0000 chunk 72 optimal weight: 50.0000 chunk 96 optimal weight: 10.0000 chunk 69 optimal weight: 5.9990 chunk 98 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 87 optimal weight: 20.0000 chunk 78 optimal weight: 10.0000 overall best weight: 6.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 85 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.068757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2916 r_free = 0.2916 target = 0.046480 restraints weight = 54460.875| |-----------------------------------------------------------------------------| r_work (start): 0.2818 rms_B_bonded: 2.81 r_work (final): 0.2818 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8668 moved from start: 0.4269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.079 12629 Z= 0.438 Angle : 0.904 9.712 18303 Z= 0.481 Chirality : 0.058 0.259 2089 Planarity : 0.006 0.050 1310 Dihedral : 34.022 100.673 3979 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 13.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 5.66 % Allowed : 17.48 % Favored : 76.86 % 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: 2.05 (0.30), residues: 730 helix: 1.97 (0.21), residues: 550 sheet: None (None), residues: 0 loop : -0.53 (0.44), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG G 89 TYR 0.017 0.003 TYR G 40 PHE 0.023 0.003 PHE G 26 HIS 0.010 0.002 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00904 / 0.44 (12629) covalent geometry : angle 0.90402 / 0.48 (18303) hydrogen bonds : bond 0.09880 / 6.81 ( 737) hydrogen bonds : angle 3.84247 / 2.79 ( 1867) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 153 time to evaluate : 0.307 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 22 LEU cc_start: 0.7146 (OUTLIER) cc_final: 0.6463 (mt) REVERT: B 84 MET cc_start: 0.8905 (mmm) cc_final: 0.8687 (mmm) REVERT: C 92 GLU cc_start: 0.9009 (tp30) cc_final: 0.8247 (tp30) REVERT: C 96 LYS cc_start: 0.9003 (mmmt) cc_final: 0.8162 (mmmt) REVERT: D 91 ASP cc_start: 0.9091 (t0) cc_final: 0.8779 (t0) REVERT: D 116 GLU cc_start: 0.8837 (mp0) cc_final: 0.8239 (mp0) REVERT: E 42 ARG cc_start: 0.8243 (mtp180) cc_final: 0.7854 (ttm-80) REVERT: G 39 LYS cc_start: 0.9592 (mmmm) cc_final: 0.9207 (mmmm) REVERT: G 85 GLN cc_start: 0.8926 (OUTLIER) cc_final: 0.8397 (tm-30) REVERT: G 91 ASP cc_start: 0.8840 (t0) cc_final: 0.8402 (t0) REVERT: G 93 GLU cc_start: 0.8856 (mm-30) cc_final: 0.8472 (mm-30) REVERT: H 58 GLU cc_start: 0.8328 (mm-30) cc_final: 0.8028 (mm-30) REVERT: H 74 ASP cc_start: 0.9116 (p0) cc_final: 0.8782 (p0) REVERT: H 91 ASP cc_start: 0.9013 (t0) cc_final: 0.8666 (t0) REVERT: H 116 GLU cc_start: 0.8822 (mp0) cc_final: 0.8213 (mp0) REVERT: H 146 SER cc_start: 0.9357 (m) cc_final: 0.9060 (p) outliers start: 35 outliers final: 18 residues processed: 177 average time/residue: 0.1089 time to fit residues: 26.3187 Evaluate side-chains 162 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 142 time to evaluate : 0.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain B residue 74 GLU Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain D residue 62 ILE Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain F residue 22 LEU Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 85 GLN Chi-restraints excluded: chain G residue 88 VAL Chi-restraints excluded: chain G residue 102 THR Chi-restraints excluded: chain H residue 57 VAL Chi-restraints excluded: chain H residue 62 ILE Chi-restraints excluded: chain H residue 111 THR Chi-restraints excluded: chain H residue 136 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 25 optimal weight: 4.9990 chunk 56 optimal weight: 0.9980 chunk 88 optimal weight: 20.0000 chunk 47 optimal weight: 1.9990 chunk 45 optimal weight: 0.9980 chunk 9 optimal weight: 0.9990 chunk 92 optimal weight: 10.0000 chunk 40 optimal weight: 1.9990 chunk 86 optimal weight: 40.0000 chunk 97 optimal weight: 20.0000 chunk 24 optimal weight: 0.9980 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 93 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.070880 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.048149 restraints weight = 53432.500| |-----------------------------------------------------------------------------| r_work (start): 0.2877 rms_B_bonded: 2.66 r_work (final): 0.2877 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8612 moved from start: 0.4339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 12629 Z= 0.146 Angle : 0.650 10.704 18303 Z= 0.369 Chirality : 0.046 0.231 2089 Planarity : 0.004 0.049 1310 Dihedral : 33.646 105.365 3979 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 10.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 2.75 % Allowed : 20.87 % Favored : 76.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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 (0.31), residues: 730 helix: 2.47 (0.22), residues: 550 sheet: None (None), residues: 0 loop : -0.37 (0.44), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 23 TYR 0.028 0.002 TYR B 88 PHE 0.011 0.001 PHE A 67 HIS 0.004 0.001 HIS D 72 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.15 (12629) covalent geometry : angle 0.64998 / 0.37 (18303) hydrogen bonds : bond 0.04534 / 3.17 ( 737) hydrogen bonds : angle 3.25241 / 2.37 ( 1867) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 171 time to evaluate : 0.282 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 88 TYR cc_start: 0.9215 (m-80) cc_final: 0.8467 (m-10) REVERT: C 85 GLN cc_start: 0.9042 (OUTLIER) cc_final: 0.8684 (tm-30) REVERT: D 91 ASP cc_start: 0.9101 (t0) cc_final: 0.8789 (t0) REVERT: D 94 GLU cc_start: 0.8887 (tp30) cc_final: 0.8423 (tp30) REVERT: D 98 GLN cc_start: 0.9278 (mm110) cc_final: 0.8735 (mm-40) REVERT: D 116 GLU cc_start: 0.8717 (mp0) cc_final: 0.8107 (mp0) REVERT: E 42 ARG cc_start: 0.8221 (mtp180) cc_final: 0.7582 (ttm-80) REVERT: G 39 LYS cc_start: 0.9581 (mmmm) cc_final: 0.9265 (mmmm) REVERT: G 57 GLU cc_start: 0.9019 (OUTLIER) cc_final: 0.8538 (tt0) REVERT: G 85 GLN cc_start: 0.9017 (OUTLIER) cc_final: 0.8371 (tm-30) REVERT: G 91 ASP cc_start: 0.8747 (t0) cc_final: 0.8454 (t70) REVERT: G 93 GLU cc_start: 0.8858 (mm-30) cc_final: 0.8566 (mm-30) REVERT: H 58 GLU cc_start: 0.8093 (mm-30) cc_final: 0.7771 (mm-30) REVERT: H 74 ASP cc_start: 0.8996 (p0) cc_final: 0.8625 (p0) REVERT: H 91 ASP cc_start: 0.9014 (t0) cc_final: 0.8700 (t0) REVERT: H 94 GLU cc_start: 0.9025 (tp30) cc_final: 0.8722 (tp30) REVERT: H 116 GLU cc_start: 0.8666 (mp0) cc_final: 0.8090 (mp0) outliers start: 17 outliers final: 10 residues processed: 181 average time/residue: 0.1094 time to fit residues: 27.2629 Evaluate side-chains 178 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 165 time to evaluate : 0.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 74 GLU Chi-restraints excluded: chain C residue 85 GLN Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain D residue 62 ILE Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain F residue 22 LEU Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 44 LYS Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 57 GLU Chi-restraints excluded: chain G residue 85 GLN Chi-restraints excluded: chain H residue 62 ILE Chi-restraints excluded: chain H residue 136 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 34 optimal weight: 2.9990 chunk 86 optimal weight: 40.0000 chunk 51 optimal weight: 0.9990 chunk 42 optimal weight: 2.9990 chunk 76 optimal weight: 20.0000 chunk 82 optimal weight: 20.0000 chunk 83 optimal weight: 20.0000 chunk 72 optimal weight: 50.0000 chunk 58 optimal weight: 0.8980 chunk 96 optimal weight: 10.0000 chunk 28 optimal weight: 5.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 85 GLN ** E 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.069947 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.047905 restraints weight = 53947.094| |-----------------------------------------------------------------------------| r_work (start): 0.2859 rms_B_bonded: 2.61 r_work (final): 0.2859 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8624 moved from start: 0.4542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 12629 Z= 0.214 Angle : 0.680 10.188 18303 Z= 0.380 Chirality : 0.046 0.215 2089 Planarity : 0.005 0.048 1310 Dihedral : 33.418 106.227 3979 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 12.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 2.75 % Allowed : 23.46 % Favored : 73.79 % 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: 2.70 (0.31), residues: 730 helix: 2.47 (0.22), residues: 550 sheet: None (None), residues: 0 loop : -0.40 (0.45), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 89 TYR 0.028 0.003 TYR G 40 PHE 0.011 0.002 PHE A 67 HIS 0.004 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00433 / 0.21 (12629) covalent geometry : angle 0.68003 / 0.38 (18303) hydrogen bonds : bond 0.05364 / 3.73 ( 737) hydrogen bonds : angle 3.29354 / 2.39 ( 1867) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 164 time to evaluate : 0.342 Fit side-chains revert: symmetry clash REVERT: C 85 GLN cc_start: 0.9129 (OUTLIER) cc_final: 0.8668 (tm-30) REVERT: D 91 ASP cc_start: 0.9074 (t0) cc_final: 0.8768 (t0) REVERT: D 94 GLU cc_start: 0.8963 (tp30) cc_final: 0.8580 (tp30) REVERT: D 98 GLN cc_start: 0.9293 (mm110) cc_final: 0.8932 (mm-40) REVERT: D 116 GLU cc_start: 0.8768 (mp0) cc_final: 0.8118 (mp0) REVERT: E 42 ARG cc_start: 0.8249 (mtp180) cc_final: 0.7784 (ttm110) REVERT: F 88 TYR cc_start: 0.9239 (m-10) cc_final: 0.7968 (m-80) REVERT: G 39 LYS cc_start: 0.9586 (mmmm) cc_final: 0.9212 (mmmm) REVERT: G 85 GLN cc_start: 0.9032 (OUTLIER) cc_final: 0.8352 (tm-30) REVERT: G 91 ASP cc_start: 0.8742 (t0) cc_final: 0.8353 (t0) REVERT: G 93 GLU cc_start: 0.8898 (mm-30) cc_final: 0.8616 (mm-30) REVERT: H 58 GLU cc_start: 0.8182 (mm-30) cc_final: 0.7874 (mm-30) REVERT: H 74 ASP cc_start: 0.9006 (p0) cc_final: 0.8653 (p0) REVERT: H 91 ASP cc_start: 0.9032 (t0) cc_final: 0.8710 (t0) REVERT: H 94 GLU cc_start: 0.8947 (tp30) cc_final: 0.8744 (tp30) REVERT: H 106 TYR cc_start: 0.8332 (m-10) cc_final: 0.7981 (m-10) REVERT: H 116 GLU cc_start: 0.8724 (mp0) cc_final: 0.8103 (mp0) REVERT: H 146 SER cc_start: 0.9261 (m) cc_final: 0.8943 (p) outliers start: 17 outliers final: 10 residues processed: 176 average time/residue: 0.1143 time to fit residues: 27.6111 Evaluate side-chains 170 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 158 time to evaluate : 0.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 74 GLU Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain C residue 85 GLN Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain D residue 62 ILE Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 85 GLN Chi-restraints excluded: chain H residue 62 ILE Chi-restraints excluded: chain H residue 136 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 92 optimal weight: 10.0000 chunk 54 optimal weight: 4.9990 chunk 12 optimal weight: 1.9990 chunk 74 optimal weight: 30.0000 chunk 36 optimal weight: 9.9990 chunk 64 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 94 optimal weight: 10.0000 chunk 86 optimal weight: 40.0000 chunk 47 optimal weight: 4.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 85 GLN ** E 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.069935 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.047323 restraints weight = 53416.132| |-----------------------------------------------------------------------------| r_work (start): 0.2854 rms_B_bonded: 2.52 r_work (final): 0.2854 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8625 moved from start: 0.4664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 12629 Z= 0.195 Angle : 0.675 10.902 18303 Z= 0.379 Chirality : 0.046 0.214 2089 Planarity : 0.005 0.064 1310 Dihedral : 33.318 107.189 3979 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 12.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 2.10 % Allowed : 24.60 % Favored : 73.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 2.63 (0.31), residues: 730 helix: 2.42 (0.22), residues: 550 sheet: None (None), residues: 0 loop : -0.44 (0.45), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 89 TYR 0.075 0.003 TYR B 88 PHE 0.009 0.001 PHE A 67 HIS 0.003 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00399 / 0.20 (12629) covalent geometry : angle 0.67470 / 0.38 (18303) hydrogen bonds : bond 0.04733 / 3.29 ( 737) hydrogen bonds : angle 3.28333 / 2.38 ( 1867) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 164 time to evaluate : 0.190 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 84 MET cc_start: 0.8260 (mmm) cc_final: 0.7943 (tpp) REVERT: C 30 ARG cc_start: 0.8507 (ttm170) cc_final: 0.8269 (ttm170) REVERT: D 91 ASP cc_start: 0.9049 (t0) cc_final: 0.8741 (t0) REVERT: D 94 GLU cc_start: 0.8966 (tp30) cc_final: 0.8536 (tp30) REVERT: D 98 GLN cc_start: 0.9281 (mm110) cc_final: 0.8893 (mm-40) REVERT: D 116 GLU cc_start: 0.8732 (mp0) cc_final: 0.8090 (mp0) REVERT: G 39 LYS cc_start: 0.9589 (mmmm) cc_final: 0.9162 (mmmm) REVERT: G 85 GLN cc_start: 0.9030 (OUTLIER) cc_final: 0.8340 (tm-30) REVERT: G 91 ASP cc_start: 0.8681 (t0) cc_final: 0.8380 (t70) REVERT: G 93 GLU cc_start: 0.8860 (mm-30) cc_final: 0.8575 (mm-30) REVERT: H 58 GLU cc_start: 0.8151 (mm-30) cc_final: 0.7840 (mm-30) REVERT: H 74 ASP cc_start: 0.8986 (p0) cc_final: 0.8627 (p0) REVERT: H 91 ASP cc_start: 0.9004 (t0) cc_final: 0.8683 (t0) REVERT: H 106 TYR cc_start: 0.8333 (m-10) cc_final: 0.7970 (m-10) REVERT: H 116 GLU cc_start: 0.8698 (mp0) cc_final: 0.8087 (mp0) REVERT: H 146 SER cc_start: 0.9262 (m) cc_final: 0.8944 (p) outliers start: 13 outliers final: 10 residues processed: 173 average time/residue: 0.1078 time to fit residues: 25.6338 Evaluate side-chains 171 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 160 time to evaluate : 0.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 74 GLU Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain D residue 62 ILE Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 85 GLN Chi-restraints excluded: chain H residue 62 ILE Chi-restraints excluded: chain H residue 136 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 19 optimal weight: 1.9990 chunk 80 optimal weight: 10.0000 chunk 17 optimal weight: 9.9990 chunk 79 optimal weight: 10.0000 chunk 96 optimal weight: 20.0000 chunk 36 optimal weight: 9.9990 chunk 89 optimal weight: 20.0000 chunk 25 optimal weight: 0.8980 chunk 5 optimal weight: 0.9980 chunk 50 optimal weight: 0.9990 chunk 98 optimal weight: 20.0000 overall best weight: 2.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.069272 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2932 r_free = 0.2932 target = 0.046385 restraints weight = 53418.030| |-----------------------------------------------------------------------------| r_work (start): 0.2843 rms_B_bonded: 2.67 r_work (final): 0.2843 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8663 moved from start: 0.4981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 12629 Z= 0.217 Angle : 0.687 11.222 18303 Z= 0.385 Chirality : 0.046 0.209 2089 Planarity : 0.005 0.047 1310 Dihedral : 33.129 110.068 3979 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 11.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 2.43 % Allowed : 24.60 % Favored : 72.98 % 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: 2.50 (0.31), residues: 730 helix: 2.30 (0.22), residues: 556 sheet: None (None), residues: 0 loop : -0.50 (0.46), residues: 174 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 67 TYR 0.067 0.003 TYR B 88 PHE 0.009 0.001 PHE G 26 HIS 0.006 0.001 HIS D 72 Details of bonding type rmsd/Z covalent geometry : bond 0.00442 / 0.22 (12629) covalent geometry : angle 0.68666 / 0.38 (18303) hydrogen bonds : bond 0.05132 / 3.57 ( 737) hydrogen bonds : angle 3.39302 / 2.47 ( 1867) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 162 time to evaluate : 0.305 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 84 MET cc_start: 0.8287 (mmm) cc_final: 0.7924 (tpp) REVERT: D 91 ASP cc_start: 0.9068 (t0) cc_final: 0.8770 (t0) REVERT: D 94 GLU cc_start: 0.8973 (tp30) cc_final: 0.8538 (tp30) REVERT: D 98 GLN cc_start: 0.9273 (mm110) cc_final: 0.8911 (mm-40) REVERT: D 116 GLU cc_start: 0.8718 (mp0) cc_final: 0.8131 (mp0) REVERT: E 42 ARG cc_start: 0.8314 (mtp180) cc_final: 0.7859 (ttm110) REVERT: G 39 LYS cc_start: 0.9584 (mmmm) cc_final: 0.9162 (mmmm) REVERT: G 85 GLN cc_start: 0.9009 (OUTLIER) cc_final: 0.8307 (tm-30) REVERT: G 91 ASP cc_start: 0.8719 (t0) cc_final: 0.8351 (t0) REVERT: G 93 GLU cc_start: 0.8877 (mm-30) cc_final: 0.8603 (mm-30) REVERT: H 58 GLU cc_start: 0.8221 (mm-30) cc_final: 0.7867 (mm-30) REVERT: H 74 ASP cc_start: 0.9031 (p0) cc_final: 0.8695 (p0) REVERT: H 91 ASP cc_start: 0.9012 (t0) cc_final: 0.8701 (t0) REVERT: H 116 GLU cc_start: 0.8705 (mp0) cc_final: 0.8093 (mp0) REVERT: H 146 SER cc_start: 0.9257 (m) cc_final: 0.8942 (p) outliers start: 15 outliers final: 11 residues processed: 173 average time/residue: 0.1220 time to fit residues: 29.0225 Evaluate side-chains 166 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 154 time to evaluate : 0.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 44 LYS Chi-restraints excluded: chain B residue 74 GLU Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain D residue 62 ILE Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 85 GLN Chi-restraints excluded: chain H residue 62 ILE Chi-restraints excluded: chain H residue 136 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 87 optimal weight: 40.0000 chunk 82 optimal weight: 20.0000 chunk 47 optimal weight: 0.6980 chunk 41 optimal weight: 0.8980 chunk 24 optimal weight: 1.9990 chunk 33 optimal weight: 0.9980 chunk 84 optimal weight: 20.0000 chunk 85 optimal weight: 50.0000 chunk 50 optimal weight: 1.9990 chunk 23 optimal weight: 0.6980 chunk 25 optimal weight: 0.3980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 75 HIS ** E 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.070104 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.047690 restraints weight = 52555.699| |-----------------------------------------------------------------------------| r_work (start): 0.2882 rms_B_bonded: 2.62 r_work (final): 0.2882 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8628 moved from start: 0.5053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 12629 Z= 0.135 Angle : 0.647 11.702 18303 Z= 0.369 Chirality : 0.044 0.233 2089 Planarity : 0.005 0.053 1310 Dihedral : 32.962 110.702 3979 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 10.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 1.78 % Allowed : 25.40 % Favored : 72.82 % 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: 2.62 (0.31), residues: 730 helix: 2.40 (0.22), residues: 554 sheet: None (None), residues: 0 loop : -0.45 (0.46), residues: 176 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 89 TYR 0.070 0.003 TYR B 88 PHE 0.011 0.001 PHE A 67 HIS 0.005 0.001 HIS D 72 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.14 (12629) covalent geometry : angle 0.64747 / 0.37 (18303) hydrogen bonds : bond 0.04126 / 2.88 ( 737) hydrogen bonds : angle 3.22151 / 2.34 ( 1867) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2051.59 seconds wall clock time: 35 minutes 57.75 seconds (2157.75 seconds total)