Starting phenix.real_space_refine on Wed Aug 5 19:48:23 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9k42_62040/08_2026/9k42_62040.cif Found real_map, /net/cci-nas-00/data/ceres_data/9k42_62040/08_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_62040/08_2026/9k42_62040.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9k42_62040/08_2026/9k42_62040.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9k42_62040/08_2026/9k42_62040.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9k42_62040/08_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-2.2rc3-6140/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: 2.18, per 1000 atoms: 0.18 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: 0.94 Conformation dependent library (CDL) restraints added in 230.0 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: 2.16 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: 1.75 Time building geometry restraints manager: 1.28 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 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=" O3' DG J 27 " pdb=" P DA J 28 " ideal model delta sigma weight residual 1.607 1.592 0.015 1.20e-02 6.94e+03 1.49e+00 bond pdb=" O3' DC I -56 " pdb=" P DG I -55 " ideal model delta sigma weight residual 1.607 1.593 0.014 1.20e-02 6.94e+03 1.35e+00 bond pdb=" O3' DC I -27 " pdb=" P DT I -26 " ideal model delta sigma weight residual 1.607 1.593 0.014 1.20e-02 6.94e+03 1.33e+00 bond pdb=" O3' DT I 68 " pdb=" P DC I 69 " ideal model delta sigma weight residual 1.607 1.593 0.014 1.20e-02 6.94e+03 1.30e+00 bond pdb=" O3' DG I 27 " pdb=" P DG I 28 " ideal model delta sigma weight residual 1.607 1.593 0.014 1.20e-02 6.94e+03 1.29e+00 ... (remaining 12624 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.92: 17778 1.92 - 3.84: 485 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: 1.080 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: 0.190 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 12.220 Find NCS groups from input model: 0.090 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:1.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.900 ------------------------------------------------------------------------------- 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= 0.275 Angle : 0.733 9.601 18303 Z= 0.526 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 0.73328 / 0.53 (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 : 0.301 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: D 56 ASN cc_start: 0.8420 (m-40) cc_final: 0.8076 (t0) 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: 0.1215 time to fit residues: 33.2245 Evaluate side-chains 158 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 156 time to evaluate : 0.229 ------------------------------------------------------------------------------- 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: 1.9990 chunk 61 optimal weight: 7.9990 chunk 45 optimal weight: 0.0980 overall best weight: 1.7786 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** C 85 GLN C 105 ASN E 39 HIS E 108 ASN G 25 GLN G 85 GLN H 56 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.078006 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.055924 restraints weight = 53775.021| |-----------------------------------------------------------------------------| r_work (start): 0.3071 rms_B_bonded: 2.70 r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 moved from start: 0.2009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12629 Z= 0.180 Angle : 0.822 9.504 18303 Z= 0.441 Chirality : 0.057 0.269 2089 Planarity : 0.005 0.056 1310 Dihedral : 34.593 89.462 3984 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % Rotamer: Outliers : 3.07 % Allowed : 17.48 % Favored : 79.45 % 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: 2.59 (0.30), residues: 730 helix: 2.35 (0.21), residues: 548 sheet: None (None), residues: 0 loop : -0.26 (0.41), residues: 182 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 43 TYR 0.023 0.003 TYR D 106 PHE 0.011 0.001 PHE A 67 HIS 0.009 0.002 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.18 (12629) covalent geometry : angle 0.82231 / 0.44 (18303) hydrogen bonds : bond 0.05775 / 4.01 ( 737) hydrogen bonds : angle 3.44566 / 2.50 ( 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 195 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 176 time to evaluate : 0.313 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 LEU cc_start: 0.9225 (mt) cc_final: 0.8987 (mt) REVERT: A 97 GLU cc_start: 0.8068 (mt-10) cc_final: 0.7728 (mt-10) REVERT: C 91 ASP cc_start: 0.7824 (t70) cc_final: 0.7622 (t70) REVERT: D 56 ASN cc_start: 0.8562 (m-40) cc_final: 0.8098 (t0) REVERT: D 82 MET cc_start: 0.9180 (tpp) cc_final: 0.8949 (tpp) REVERT: D 91 ASP cc_start: 0.9021 (t0) cc_final: 0.8745 (t0) REVERT: E 42 ARG cc_start: 0.8154 (mtp180) cc_final: 0.7700 (ttm-80) REVERT: E 97 GLU cc_start: 0.8052 (mt-10) cc_final: 0.7693 (mt-10) REVERT: F 88 TYR cc_start: 0.9332 (m-10) cc_final: 0.8537 (m-80) REVERT: G 65 GLU cc_start: 0.8425 (tm-30) cc_final: 0.8162 (tm-30) REVERT: G 93 GLU cc_start: 0.8570 (mm-30) cc_final: 0.8174 (mm-30) REVERT: H 74 ASP cc_start: 0.8967 (p0) cc_final: 0.8625 (p0) REVERT: H 91 ASP cc_start: 0.8915 (t0) cc_final: 0.8643 (t0) REVERT: H 94 GLU cc_start: 0.8842 (mm-30) cc_final: 0.8458 (mm-30) REVERT: H 106 TYR cc_start: 0.8369 (m-10) cc_final: 0.7829 (m-10) REVERT: H 116 GLU cc_start: 0.8299 (mp0) cc_final: 0.7983 (mp0) REVERT: H 146 SER cc_start: 0.9222 (m) cc_final: 0.8910 (p) outliers start: 19 outliers final: 12 residues processed: 185 average time/residue: 0.1094 time to fit residues: 27.8041 Evaluate side-chains 175 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 163 time to evaluate : 0.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain D residue 113 THR Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain F residue 22 LEU Chi-restraints excluded: chain F residue 74 GLU 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: 8.9990 chunk 15 optimal weight: 4.9990 chunk 9 optimal weight: 0.0870 chunk 92 optimal weight: 10.0000 chunk 56 optimal weight: 3.9990 chunk 54 optimal weight: 0.7980 chunk 88 optimal weight: 20.0000 chunk 95 optimal weight: 9.9990 chunk 48 optimal weight: 3.9990 chunk 24 optimal weight: 3.9990 chunk 17 optimal weight: 10.0000 overall best weight: 2.5764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 74 ASN D 107 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.074842 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.052478 restraints weight = 53869.892| |-----------------------------------------------------------------------------| r_work (start): 0.2984 rms_B_bonded: 2.70 r_work (final): 0.2984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8471 moved from start: 0.2740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.081 12629 Z= 0.196 Angle : 0.690 8.193 18303 Z= 0.388 Chirality : 0.050 0.246 2089 Planarity : 0.005 0.050 1310 Dihedral : 34.294 98.890 3979 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 10.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 3.88 % Allowed : 17.15 % Favored : 78.96 % 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: 2.66 (0.30), residues: 730 helix: 2.42 (0.21), residues: 548 sheet: None (None), residues: 0 loop : -0.32 (0.42), residues: 182 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 30 TYR 0.016 0.003 TYR G 58 PHE 0.012 0.002 PHE E 67 HIS 0.003 0.001 HIS D 72 Details of bonding type rmsd/Z covalent geometry : bond 0.00384 / 0.20 (12629) covalent geometry : angle 0.69043 / 0.39 (18303) hydrogen bonds : bond 0.05241 / 3.64 ( 737) hydrogen bonds : angle 3.34679 / 2.43 ( 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 191 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 167 time to evaluate : 0.187 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 76 GLN cc_start: 0.8943 (tm-30) cc_final: 0.8585 (tm-30) REVERT: C 74 ASN cc_start: 0.8902 (OUTLIER) cc_final: 0.8524 (t0) REVERT: C 91 ASP cc_start: 0.7918 (t70) cc_final: 0.7650 (t70) REVERT: C 92 GLU cc_start: 0.8998 (tp30) cc_final: 0.8027 (tp30) REVERT: C 96 LYS cc_start: 0.8997 (mmmt) cc_final: 0.8228 (mmmt) REVERT: D 56 ASN cc_start: 0.8728 (m-40) cc_final: 0.8277 (t0) REVERT: D 91 ASP cc_start: 0.9046 (t0) cc_final: 0.8662 (t0) REVERT: D 98 GLN cc_start: 0.9308 (mm-40) cc_final: 0.9060 (mm-40) REVERT: D 116 GLU cc_start: 0.8601 (mp0) cc_final: 0.8135 (mp0) REVERT: E 42 ARG cc_start: 0.8131 (mtp180) cc_final: 0.7606 (ttm-80) REVERT: E 58 THR cc_start: 0.9561 (OUTLIER) cc_final: 0.9353 (t) REVERT: E 76 GLN cc_start: 0.8952 (tm-30) cc_final: 0.8623 (tm-30) REVERT: F 88 TYR cc_start: 0.9207 (m-10) cc_final: 0.8984 (m-80) REVERT: G 91 ASP cc_start: 0.8658 (t0) cc_final: 0.8364 (t70) REVERT: G 93 GLU cc_start: 0.8744 (mm-30) cc_final: 0.8490 (mm-30) REVERT: H 58 GLU cc_start: 0.7927 (mm-30) cc_final: 0.7707 (mm-30) REVERT: H 74 ASP cc_start: 0.9012 (p0) cc_final: 0.8623 (p0) REVERT: H 91 ASP cc_start: 0.8999 (t0) cc_final: 0.8604 (t0) REVERT: H 94 GLU cc_start: 0.8963 (mm-30) cc_final: 0.8727 (mm-30) REVERT: H 116 GLU cc_start: 0.8552 (mp0) cc_final: 0.8134 (mp0) REVERT: H 146 SER cc_start: 0.9224 (m) cc_final: 0.8900 (p) outliers start: 24 outliers final: 17 residues processed: 181 average time/residue: 0.1151 time to fit residues: 28.9248 Evaluate side-chains 175 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 156 time to evaluate : 0.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 74 GLU Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 74 ASN 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 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 30 THR Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 57 GLU Chi-restraints excluded: chain G residue 102 THR 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 112 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: 0.9990 chunk 94 optimal weight: 10.0000 chunk 3 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 86 optimal weight: 40.0000 chunk 82 optimal weight: 20.0000 chunk 67 optimal weight: 6.9990 chunk 95 optimal weight: 20.0000 chunk 20 optimal weight: 1.9990 chunk 85 optimal weight: 50.0000 chunk 35 optimal weight: 1.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 98 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.074674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.051606 restraints weight = 52913.198| |-----------------------------------------------------------------------------| r_work (start): 0.2971 rms_B_bonded: 2.76 r_work (final): 0.2971 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8499 moved from start: 0.3033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 12629 Z= 0.159 Angle : 0.641 9.861 18303 Z= 0.364 Chirality : 0.046 0.231 2089 Planarity : 0.005 0.047 1310 Dihedral : 33.969 96.592 3979 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 10.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 3.40 % Allowed : 17.80 % Favored : 78.80 % 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 0.006 0.000 ARG D 105 TYR 0.015 0.002 TYR B 88 PHE 0.012 0.001 PHE E 67 HIS 0.004 0.001 HIS D 72 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.16 (12629) covalent geometry : angle 0.64055 / 0.36 (18303) hydrogen bonds : bond 0.04479 / 3.13 ( 737) hydrogen bonds : angle 3.18239 / 2.31 ( 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 188 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 167 time to evaluate : 0.303 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 22 LEU cc_start: 0.7298 (OUTLIER) cc_final: 0.6696 (mt) REVERT: C 92 GLU cc_start: 0.9073 (tp30) cc_final: 0.8050 (tp30) REVERT: C 96 LYS cc_start: 0.9039 (mmmt) cc_final: 0.8325 (mmmt) REVERT: D 56 ASN cc_start: 0.8831 (m-40) cc_final: 0.8374 (t0) REVERT: D 91 ASP cc_start: 0.9060 (t0) cc_final: 0.8697 (t0) REVERT: D 94 GLU cc_start: 0.8750 (tp30) cc_final: 0.8235 (tp30) REVERT: D 98 GLN cc_start: 0.9237 (mm110) cc_final: 0.8826 (mm-40) REVERT: D 106 TYR cc_start: 0.8207 (m-10) cc_final: 0.7931 (m-80) REVERT: D 116 GLU cc_start: 0.8597 (mp0) cc_final: 0.8134 (mp0) REVERT: E 42 ARG cc_start: 0.8081 (mtp180) cc_final: 0.7783 (ttm-80) REVERT: F 88 TYR cc_start: 0.9249 (m-10) cc_final: 0.9037 (m-80) REVERT: G 85 GLN cc_start: 0.8867 (OUTLIER) cc_final: 0.8507 (tm-30) REVERT: G 91 ASP cc_start: 0.8784 (t0) cc_final: 0.8515 (t70) REVERT: G 93 GLU cc_start: 0.8768 (mm-30) cc_final: 0.8449 (mm-30) REVERT: H 58 GLU cc_start: 0.7896 (mm-30) cc_final: 0.7659 (mm-30) REVERT: H 74 ASP cc_start: 0.9010 (p0) cc_final: 0.8626 (p0) REVERT: H 82 MET cc_start: 0.9256 (tpp) cc_final: 0.9016 (tpp) REVERT: H 91 ASP cc_start: 0.8999 (t0) cc_final: 0.8606 (t0) REVERT: H 94 GLU cc_start: 0.8873 (mm-30) cc_final: 0.8650 (mm-30) REVERT: H 116 GLU cc_start: 0.8538 (mp0) cc_final: 0.8116 (mp0) REVERT: H 146 SER cc_start: 0.9187 (m) cc_final: 0.8885 (p) outliers start: 21 outliers final: 10 residues processed: 179 average time/residue: 0.1029 time to fit residues: 25.7633 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 : 0.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain B residue 74 GLU Chi-restraints excluded: chain B residue 96 THR 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 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 111 THR 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: 0.9980 chunk 48 optimal weight: 0.9990 chunk 28 optimal weight: 6.9990 chunk 12 optimal weight: 4.9990 chunk 27 optimal weight: 5.9990 chunk 2 optimal weight: 0.9980 chunk 94 optimal weight: 9.9990 chunk 90 optimal weight: 9.9990 chunk 35 optimal weight: 4.9990 chunk 62 optimal weight: 20.0000 overall best weight: 2.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 55 GLN E 93 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.072740 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.049199 restraints weight = 53442.319| |-----------------------------------------------------------------------------| r_work (start): 0.2913 rms_B_bonded: 2.68 r_work (final): 0.2913 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8573 moved from start: 0.3627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 12629 Z= 0.200 Angle : 0.676 11.302 18303 Z= 0.377 Chirality : 0.047 0.215 2089 Planarity : 0.005 0.049 1310 Dihedral : 33.755 98.594 3979 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 11.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 4.37 % Allowed : 17.80 % Favored : 77.83 % 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: 2.80 (0.31), residues: 730 helix: 2.54 (0.22), residues: 550 sheet: None (None), residues: 0 loop : -0.36 (0.44), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 30 TYR 0.016 0.002 TYR B 88 PHE 0.013 0.002 PHE A 67 HIS 0.003 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00394 / 0.20 (12629) covalent geometry : angle 0.67570 / 0.38 (18303) hydrogen bonds : bond 0.05193 / 3.61 ( 737) hydrogen bonds : angle 3.23849 / 2.34 ( 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 195 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 168 time to evaluate : 0.187 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 22 LEU cc_start: 0.7321 (OUTLIER) cc_final: 0.7015 (mt) REVERT: B 88 TYR cc_start: 0.9251 (m-80) cc_final: 0.8912 (m-80) REVERT: C 91 ASP cc_start: 0.8699 (t70) cc_final: 0.8442 (t70) REVERT: C 92 GLU cc_start: 0.8952 (tp30) cc_final: 0.8232 (tp30) REVERT: C 96 LYS cc_start: 0.8995 (mmmt) cc_final: 0.8087 (mmmt) REVERT: C 109 MET cc_start: 0.7064 (mmm) cc_final: 0.6576 (mpp) REVERT: D 56 ASN cc_start: 0.8980 (m-40) cc_final: 0.8408 (t0) REVERT: D 58 GLU cc_start: 0.7773 (OUTLIER) cc_final: 0.6749 (mm-30) REVERT: D 91 ASP cc_start: 0.9066 (t0) cc_final: 0.8712 (t0) REVERT: D 94 GLU cc_start: 0.8709 (tp30) cc_final: 0.8103 (tp30) REVERT: D 98 GLN cc_start: 0.9216 (mm110) cc_final: 0.8797 (mm-40) REVERT: D 116 GLU cc_start: 0.8670 (mp0) cc_final: 0.8158 (mp0) REVERT: E 42 ARG cc_start: 0.8153 (mtp180) cc_final: 0.7836 (ttm-80) REVERT: G 39 LYS cc_start: 0.9557 (mmmm) cc_final: 0.9233 (mmmm) REVERT: G 91 ASP cc_start: 0.8763 (t0) cc_final: 0.8496 (t70) REVERT: G 93 GLU cc_start: 0.8812 (mm-30) cc_final: 0.8543 (mm-30) REVERT: H 58 GLU cc_start: 0.8070 (mm-30) cc_final: 0.7805 (mm-30) REVERT: H 74 ASP cc_start: 0.9030 (p0) cc_final: 0.8657 (p0) REVERT: H 82 MET cc_start: 0.9291 (tpp) cc_final: 0.9083 (tpp) REVERT: H 91 ASP cc_start: 0.9027 (t0) cc_final: 0.8629 (t0) REVERT: H 94 GLU cc_start: 0.8913 (mm-30) cc_final: 0.8674 (tp30) REVERT: H 116 GLU cc_start: 0.8598 (mp0) cc_final: 0.8114 (mp0) REVERT: H 146 SER cc_start: 0.9206 (m) cc_final: 0.8888 (p) outliers start: 27 outliers final: 15 residues processed: 187 average time/residue: 0.1229 time to fit residues: 31.1809 Evaluate side-chains 172 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 155 time to evaluate : 0.310 ------------------------------------------------------------------------------- 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 74 GLU Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain D residue 58 GLU Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain D residue 62 ILE Chi-restraints excluded: chain E residue 76 GLN 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 96 THR 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 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: 0.9980 chunk 27 optimal weight: 0.0870 chunk 92 optimal weight: 10.0000 chunk 72 optimal weight: 50.0000 chunk 96 optimal weight: 10.0000 chunk 69 optimal weight: 0.9990 chunk 98 optimal weight: 20.0000 chunk 0 optimal weight: 10.0000 chunk 87 optimal weight: 30.0000 chunk 78 optimal weight: 10.0000 overall best weight: 4.4168 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 55 GLN ** E 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 93 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 = 0.3539 r_free = 0.3539 target = 0.069596 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2936 r_free = 0.2936 target = 0.046908 restraints weight = 54190.576| |-----------------------------------------------------------------------------| r_work (start): 0.2839 rms_B_bonded: 2.69 r_work (final): 0.2839 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8654 moved from start: 0.4316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.071 12629 Z= 0.294 Angle : 0.765 9.861 18303 Z= 0.417 Chirality : 0.051 0.244 2089 Planarity : 0.006 0.139 1310 Dihedral : 33.669 101.449 3979 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 12.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % Rotamer: Outliers : 3.88 % Allowed : 20.23 % Favored : 75.89 % 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: 2.30 (0.31), residues: 730 helix: 2.19 (0.22), residues: 550 sheet: None (None), residues: 0 loop : -0.60 (0.44), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG H 105 TYR 0.033 0.003 TYR F 88 PHE 0.011 0.002 PHE G 26 HIS 0.006 0.002 HIS H 72 Details of bonding type rmsd/Z covalent geometry : bond 0.00606 / 0.29 (12629) covalent geometry : angle 0.76547 / 0.42 (18303) hydrogen bonds : bond 0.06411 / 4.42 ( 737) hydrogen bonds : angle 3.49036 / 2.52 ( 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 182 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 158 time to evaluate : 0.308 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 PHE cc_start: 0.8680 (m-80) cc_final: 0.8353 (m-80) REVERT: A 97 GLU cc_start: 0.8188 (mt-10) cc_final: 0.7883 (mt-10) REVERT: B 22 LEU cc_start: 0.7205 (OUTLIER) cc_final: 0.6863 (mt) REVERT: C 91 ASP cc_start: 0.8743 (t70) cc_final: 0.8529 (t0) REVERT: C 92 GLU cc_start: 0.9017 (tp30) cc_final: 0.8408 (tp30) REVERT: C 96 LYS cc_start: 0.8984 (mmmt) cc_final: 0.8068 (mmmt) REVERT: C 109 MET cc_start: 0.7262 (mmm) cc_final: 0.6954 (mpp) REVERT: D 56 ASN cc_start: 0.8984 (m-40) cc_final: 0.8455 (t0) REVERT: D 91 ASP cc_start: 0.9088 (t0) cc_final: 0.8782 (t0) REVERT: D 94 GLU cc_start: 0.8804 (tp30) cc_final: 0.8215 (tp30) REVERT: D 98 GLN cc_start: 0.9224 (mm110) cc_final: 0.8680 (mm-40) REVERT: D 116 GLU cc_start: 0.8792 (mp0) cc_final: 0.8166 (mp0) REVERT: E 42 ARG cc_start: 0.8276 (mtp180) cc_final: 0.7951 (ttm-80) REVERT: F 88 TYR cc_start: 0.9212 (m-10) cc_final: 0.8827 (m-80) REVERT: G 39 LYS cc_start: 0.9588 (mmmm) cc_final: 0.9246 (mmmm) REVERT: G 85 GLN cc_start: 0.8944 (OUTLIER) cc_final: 0.8400 (tm-30) REVERT: G 91 ASP cc_start: 0.8821 (t0) cc_final: 0.8492 (t0) REVERT: G 93 GLU cc_start: 0.8894 (mm-30) cc_final: 0.8466 (mm-30) REVERT: H 58 GLU cc_start: 0.8211 (mm-30) cc_final: 0.7888 (mm-30) REVERT: H 74 ASP cc_start: 0.9036 (p0) cc_final: 0.8670 (p0) REVERT: H 91 ASP cc_start: 0.9026 (t0) cc_final: 0.8681 (t0) REVERT: H 116 GLU cc_start: 0.8745 (mp0) cc_final: 0.8137 (mp0) REVERT: H 146 SER cc_start: 0.9286 (m) cc_final: 0.8987 (p) outliers start: 24 outliers final: 14 residues processed: 175 average time/residue: 0.1169 time to fit residues: 27.9824 Evaluate side-chains 165 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 149 time to evaluate : 0.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 22 LEU 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 50 ILE Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 44 VAL Chi-restraints excluded: chain G residue 85 GLN 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: 0.3980 chunk 56 optimal weight: 2.9990 chunk 88 optimal weight: 20.0000 chunk 47 optimal weight: 0.1980 chunk 45 optimal weight: 1.9990 chunk 9 optimal weight: 0.9990 chunk 92 optimal weight: 10.0000 chunk 40 optimal weight: 5.9990 chunk 86 optimal weight: 50.0000 chunk 97 optimal weight: 20.0000 chunk 24 optimal weight: 0.6980 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 108 ASN D 98 GLN ** E 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 93 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.071138 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.048817 restraints weight = 53649.290| |-----------------------------------------------------------------------------| r_work (start): 0.2887 rms_B_bonded: 2.59 r_work (final): 0.2887 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8596 moved from start: 0.4398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.054 12629 Z= 0.133 Angle : 0.628 10.774 18303 Z= 0.360 Chirality : 0.045 0.225 2089 Planarity : 0.004 0.044 1310 Dihedral : 33.335 103.613 3979 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 10.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 2.10 % Allowed : 21.20 % Favored : 76.70 % 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: 2.75 (0.31), residues: 730 helix: 2.48 (0.22), residues: 550 sheet: None (None), residues: 0 loop : -0.30 (0.45), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 89 TYR 0.018 0.002 TYR B 88 PHE 0.013 0.001 PHE A 67 HIS 0.004 0.001 HIS D 72 Details of bonding type rmsd/Z covalent geometry : bond 0.00241 / 0.13 (12629) covalent geometry : angle 0.62847 / 0.36 (18303) hydrogen bonds : bond 0.04197 / 2.93 ( 737) hydrogen bonds : angle 3.15808 / 2.28 ( 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 181 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 168 time to evaluate : 0.322 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 41 PHE cc_start: 0.8652 (m-80) cc_final: 0.8376 (m-80) REVERT: A 73 GLU cc_start: 0.8533 (tt0) cc_final: 0.8264 (tt0) REVERT: B 22 LEU cc_start: 0.7013 (mt) cc_final: 0.6520 (mt) REVERT: C 65 GLU cc_start: 0.8743 (tp30) cc_final: 0.8478 (tp30) REVERT: C 91 ASP cc_start: 0.8667 (t70) cc_final: 0.8269 (t0) REVERT: C 109 MET cc_start: 0.7219 (mmm) cc_final: 0.6699 (mpp) REVERT: D 56 ASN cc_start: 0.8945 (m-40) cc_final: 0.8457 (t0) REVERT: D 91 ASP cc_start: 0.9083 (t0) cc_final: 0.8743 (t0) REVERT: D 94 GLU cc_start: 0.8685 (tp30) cc_final: 0.7863 (tp30) REVERT: D 98 GLN cc_start: 0.9174 (mm-40) cc_final: 0.8664 (mm110) REVERT: D 116 GLU cc_start: 0.8670 (mp0) cc_final: 0.8121 (mp0) REVERT: E 42 ARG cc_start: 0.8325 (mtp180) cc_final: 0.8100 (mtm110) REVERT: F 22 LEU cc_start: 0.6935 (OUTLIER) cc_final: 0.6567 (mt) REVERT: G 39 LYS cc_start: 0.9558 (mmmm) cc_final: 0.9232 (mmmm) REVERT: G 91 ASP cc_start: 0.8736 (t0) cc_final: 0.8378 (t0) REVERT: G 93 GLU cc_start: 0.8849 (mm-30) cc_final: 0.8578 (mm-30) REVERT: H 58 GLU cc_start: 0.8145 (mm-30) cc_final: 0.7825 (mm-30) REVERT: H 74 ASP cc_start: 0.8998 (p0) cc_final: 0.8648 (p0) REVERT: H 82 MET cc_start: 0.9182 (tpp) cc_final: 0.8958 (tpp) REVERT: H 91 ASP cc_start: 0.8998 (t0) cc_final: 0.8657 (t0) REVERT: H 116 GLU cc_start: 0.8621 (mp0) cc_final: 0.8086 (mp0) REVERT: H 146 SER cc_start: 0.9221 (m) cc_final: 0.8899 (p) outliers start: 13 outliers final: 7 residues processed: 177 average time/residue: 0.1322 time to fit residues: 32.1955 Evaluate side-chains 170 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 162 time to evaluate : 0.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 74 GLU Chi-restraints excluded: chain B residue 97 LEU 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 96 THR 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: 0.9980 chunk 86 optimal weight: 50.0000 chunk 51 optimal weight: 0.9990 chunk 42 optimal weight: 3.9990 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: 9.9990 chunk 96 optimal weight: 20.0000 chunk 28 optimal weight: 2.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3534 r_free = 0.3534 target = 0.069178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.046992 restraints weight = 53510.211| |-----------------------------------------------------------------------------| r_work (start): 0.2845 rms_B_bonded: 2.53 r_work (final): 0.2845 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8651 moved from start: 0.4686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 12629 Z= 0.256 Angle : 0.728 10.302 18303 Z= 0.398 Chirality : 0.048 0.225 2089 Planarity : 0.005 0.046 1310 Dihedral : 33.270 104.017 3979 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 12.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 2.43 % Allowed : 23.46 % Favored : 74.11 % 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: 2.60 (0.31), residues: 730 helix: 2.38 (0.22), residues: 550 sheet: None (None), residues: 0 loop : -0.41 (0.46), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 105 TYR 0.019 0.003 TYR F 88 PHE 0.013 0.002 PHE G 26 HIS 0.005 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00516 / 0.26 (12629) covalent geometry : angle 0.72793 / 0.40 (18303) hydrogen bonds : bond 0.06291 / 4.34 ( 737) hydrogen bonds : angle 3.42081 / 2.47 ( 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 175 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 160 time to evaluate : 0.328 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 41 PHE cc_start: 0.8675 (m-80) cc_final: 0.8407 (m-80) REVERT: A 73 GLU cc_start: 0.8513 (tt0) cc_final: 0.8268 (tt0) REVERT: B 22 LEU cc_start: 0.6882 (OUTLIER) cc_final: 0.6527 (mt) REVERT: B 88 TYR cc_start: 0.9342 (m-80) cc_final: 0.8212 (m-80) REVERT: C 65 GLU cc_start: 0.8828 (tp30) cc_final: 0.8554 (tp30) REVERT: C 109 MET cc_start: 0.7265 (mmm) cc_final: 0.6751 (mpp) REVERT: D 56 ASN cc_start: 0.8883 (m-40) cc_final: 0.8434 (t0) REVERT: D 91 ASP cc_start: 0.9059 (t0) cc_final: 0.8750 (t0) REVERT: D 94 GLU cc_start: 0.8772 (tp30) cc_final: 0.8217 (tp30) REVERT: D 98 GLN cc_start: 0.9264 (mm-40) cc_final: 0.8679 (mm-40) REVERT: D 106 TYR cc_start: 0.8190 (m-80) cc_final: 0.7579 (m-80) REVERT: D 116 GLU cc_start: 0.8773 (mp0) cc_final: 0.8131 (mp0) REVERT: E 42 ARG cc_start: 0.8354 (mtp180) cc_final: 0.8133 (mtm110) REVERT: G 39 LYS cc_start: 0.9600 (mmmm) cc_final: 0.9262 (mmmm) REVERT: G 85 GLN cc_start: 0.8958 (OUTLIER) cc_final: 0.8553 (tm-30) REVERT: G 91 ASP cc_start: 0.8761 (t0) cc_final: 0.8482 (t70) REVERT: G 93 GLU cc_start: 0.8872 (mm-30) cc_final: 0.8549 (mm-30) REVERT: H 58 GLU cc_start: 0.8302 (mm-30) cc_final: 0.7946 (mm-30) REVERT: H 74 ASP cc_start: 0.9045 (p0) cc_final: 0.8729 (p0) REVERT: H 91 ASP cc_start: 0.9000 (t0) cc_final: 0.8670 (t0) REVERT: H 94 GLU cc_start: 0.8776 (tp30) cc_final: 0.8495 (tp30) REVERT: H 116 GLU cc_start: 0.8725 (mp0) cc_final: 0.8119 (mp0) REVERT: H 146 SER cc_start: 0.9282 (m) cc_final: 0.8969 (p) outliers start: 15 outliers final: 8 residues processed: 168 average time/residue: 0.1307 time to fit residues: 30.1473 Evaluate side-chains 165 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 155 time to evaluate : 0.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain B residue 74 GLU Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain D residue 62 ILE Chi-restraints excluded: chain D residue 112 ILE Chi-restraints excluded: chain E residue 87 SER 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: 0.9980 chunk 12 optimal weight: 0.9990 chunk 74 optimal weight: 30.0000 chunk 36 optimal weight: 9.9990 chunk 64 optimal weight: 3.9990 chunk 69 optimal weight: 0.9990 chunk 27 optimal weight: 5.9990 chunk 94 optimal weight: 10.0000 chunk 86 optimal weight: 50.0000 chunk 47 optimal weight: 0.0570 overall best weight: 1.4104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 93 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 = 0.3559 r_free = 0.3559 target = 0.070270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.047212 restraints weight = 52791.437| |-----------------------------------------------------------------------------| r_work (start): 0.2874 rms_B_bonded: 2.70 r_work (final): 0.2874 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8641 moved from start: 0.4819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 12629 Z= 0.150 Angle : 0.655 11.147 18303 Z= 0.371 Chirality : 0.044 0.209 2089 Planarity : 0.004 0.045 1310 Dihedral : 33.051 105.695 3979 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 11.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 1.94 % Allowed : 24.11 % Favored : 73.95 % 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: 2.73 (0.31), residues: 730 helix: 2.42 (0.22), residues: 556 sheet: None (None), residues: 0 loop : -0.22 (0.48), residues: 174 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG G 89 TYR 0.042 0.003 TYR F 88 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 0.00286 / 0.15 (12629) covalent geometry : angle 0.65465 / 0.37 (18303) hydrogen bonds : bond 0.04260 / 2.96 ( 737) hydrogen bonds : angle 3.25718 / 2.35 ( 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: 12 poor density : 165 time to evaluate : 0.317 Fit side-chains revert: symmetry clash REVERT: A 41 PHE cc_start: 0.8585 (m-80) cc_final: 0.8309 (m-80) REVERT: A 73 GLU cc_start: 0.8530 (tt0) cc_final: 0.8302 (tt0) REVERT: B 22 LEU cc_start: 0.6944 (mt) cc_final: 0.6447 (mt) REVERT: B 88 TYR cc_start: 0.9108 (m-80) cc_final: 0.8764 (m-80) REVERT: C 65 GLU cc_start: 0.8751 (tp30) cc_final: 0.8463 (tp30) REVERT: D 56 ASN cc_start: 0.8742 (m-40) cc_final: 0.8311 (t0) REVERT: D 91 ASP cc_start: 0.9084 (t0) cc_final: 0.8774 (t0) REVERT: D 94 GLU cc_start: 0.8734 (tp30) cc_final: 0.8308 (tp30) REVERT: D 98 GLN cc_start: 0.9230 (mm-40) cc_final: 0.8981 (mm-40) REVERT: D 116 GLU cc_start: 0.8707 (mp0) cc_final: 0.8085 (mp0) REVERT: G 39 LYS cc_start: 0.9590 (mmmm) cc_final: 0.9248 (mmmm) REVERT: G 85 GLN cc_start: 0.8933 (OUTLIER) cc_final: 0.8536 (tm-30) REVERT: G 91 ASP cc_start: 0.8702 (t0) cc_final: 0.8367 (t0) REVERT: G 93 GLU cc_start: 0.8839 (mm-30) cc_final: 0.8582 (mm-30) REVERT: H 58 GLU cc_start: 0.8155 (mm-30) cc_final: 0.7820 (mm-30) REVERT: H 74 ASP cc_start: 0.8999 (p0) cc_final: 0.8668 (p0) REVERT: H 82 MET cc_start: 0.9156 (tpp) cc_final: 0.8942 (tpp) REVERT: H 91 ASP cc_start: 0.9025 (t0) cc_final: 0.8694 (t0) REVERT: H 94 GLU cc_start: 0.8695 (tp30) cc_final: 0.8236 (tp30) REVERT: H 98 GLN cc_start: 0.9183 (mm110) cc_final: 0.8633 (mm-40) REVERT: H 116 GLU cc_start: 0.8644 (mp0) cc_final: 0.8060 (mp0) REVERT: H 146 SER cc_start: 0.9227 (m) cc_final: 0.8919 (p) outliers start: 12 outliers final: 8 residues processed: 173 average time/residue: 0.1323 time to fit residues: 31.4396 Evaluate side-chains 166 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 157 time to evaluate : 0.310 ------------------------------------------------------------------------------- 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 62 ILE Chi-restraints excluded: chain E residue 87 SER 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: 0.5980 chunk 80 optimal weight: 10.0000 chunk 17 optimal weight: 10.0000 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: 0.6980 chunk 5 optimal weight: 0.9980 chunk 50 optimal weight: 6.9990 chunk 98 optimal weight: 20.0000 overall best weight: 3.8584 ------------------------------------------------------------------------------- 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 = 0.3532 r_free = 0.3532 target = 0.069043 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2921 r_free = 0.2921 target = 0.046137 restraints weight = 53855.477| |-----------------------------------------------------------------------------| r_work (start): 0.2827 rms_B_bonded: 2.70 r_work (final): 0.2827 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8676 moved from start: 0.5045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 12629 Z= 0.259 Angle : 0.741 10.456 18303 Z= 0.405 Chirality : 0.048 0.217 2089 Planarity : 0.005 0.045 1310 Dihedral : 33.044 106.531 3979 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 12.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 1.94 % Allowed : 24.43 % Favored : 73.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 2.44 (0.31), residues: 730 helix: 2.22 (0.22), residues: 556 sheet: None (None), residues: 0 loop : -0.39 (0.47), residues: 174 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG G 89 TYR 0.060 0.003 TYR F 88 PHE 0.014 0.002 PHE G 26 HIS 0.005 0.002 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00538 / 0.26 (12629) covalent geometry : angle 0.74121 / 0.41 (18303) hydrogen bonds : bond 0.06152 / 4.25 ( 737) hydrogen bonds : angle 3.49600 / 2.52 ( 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 167 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 155 time to evaluate : 0.321 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 PHE cc_start: 0.8647 (m-80) cc_final: 0.8358 (m-80) REVERT: A 73 GLU cc_start: 0.8568 (tt0) cc_final: 0.8356 (tt0) REVERT: B 22 LEU cc_start: 0.6983 (mt) cc_final: 0.6651 (mt) REVERT: B 88 TYR cc_start: 0.8979 (m-80) cc_final: 0.8711 (m-80) REVERT: C 65 GLU cc_start: 0.8844 (tp30) cc_final: 0.8559 (tp30) REVERT: D 56 ASN cc_start: 0.8713 (m-40) cc_final: 0.8317 (t0) REVERT: D 91 ASP cc_start: 0.9090 (t0) cc_final: 0.8778 (t0) REVERT: D 94 GLU cc_start: 0.8808 (tp30) cc_final: 0.8205 (tp30) REVERT: D 98 GLN cc_start: 0.9274 (mm-40) cc_final: 0.8921 (mm-40) REVERT: D 116 GLU cc_start: 0.8767 (mp0) cc_final: 0.8114 (mp0) REVERT: G 39 LYS cc_start: 0.9613 (mmmm) cc_final: 0.9266 (mmmm) REVERT: G 85 GLN cc_start: 0.8946 (OUTLIER) cc_final: 0.8527 (tm-30) REVERT: G 91 ASP cc_start: 0.8673 (t0) cc_final: 0.8282 (t0) REVERT: G 93 GLU cc_start: 0.8875 (mm-30) cc_final: 0.8584 (mm-30) REVERT: H 58 GLU cc_start: 0.8309 (mm-30) cc_final: 0.7974 (mm-30) REVERT: H 74 ASP cc_start: 0.9064 (p0) cc_final: 0.8755 (p0) REVERT: H 82 MET cc_start: 0.9217 (tpp) cc_final: 0.9002 (tpp) REVERT: H 91 ASP cc_start: 0.9024 (t0) cc_final: 0.8701 (t0) REVERT: H 94 GLU cc_start: 0.8797 (tp30) cc_final: 0.8502 (tp30) REVERT: H 116 GLU cc_start: 0.8766 (mp0) cc_final: 0.8126 (mp0) REVERT: H 146 SER cc_start: 0.9285 (m) cc_final: 0.8978 (p) outliers start: 12 outliers final: 9 residues processed: 163 average time/residue: 0.1335 time to fit residues: 29.9778 Evaluate side-chains 161 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 151 time to evaluate : 0.315 ------------------------------------------------------------------------------- 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 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: 0.9980 chunk 41 optimal weight: 0.9990 chunk 24 optimal weight: 7.9990 chunk 33 optimal weight: 0.9980 chunk 84 optimal weight: 20.0000 chunk 85 optimal weight: 40.0000 chunk 50 optimal weight: 3.9990 chunk 23 optimal weight: 1.9990 chunk 25 optimal weight: 0.7980 overall best weight: 1.1584 ------------------------------------------------------------------------------- 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** H 98 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.069916 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.047464 restraints weight = 52274.218| |-----------------------------------------------------------------------------| r_work (start): 0.2873 rms_B_bonded: 2.67 r_work (final): 0.2873 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8641 moved from start: 0.5128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 12629 Z= 0.146 Angle : 0.668 11.539 18303 Z= 0.377 Chirality : 0.044 0.211 2089 Planarity : 0.005 0.071 1310 Dihedral : 32.881 107.921 3979 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 11.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 1.62 % Allowed : 25.24 % Favored : 73.14 % 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: 2.55 (0.31), residues: 730 helix: 2.29 (0.22), residues: 556 sheet: None (None), residues: 0 loop : -0.28 (0.47), residues: 174 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG G 89 TYR 0.067 0.003 TYR F 88 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 0.00279 / 0.15 (12629) covalent geometry : angle 0.66789 / 0.38 (18303) hydrogen bonds : bond 0.04307 / 2.98 ( 737) hydrogen bonds : angle 3.29986 / 2.38 ( 1867) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2187.59 seconds wall clock time: 38 minutes 19.17 seconds (2299.17 seconds total)