Starting phenix.real_space_refine on Tue Mar 3 14:57:20 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7stf_25427/03_2026/7stf_25427.cif Found real_map, /net/cci-nas-00/data/ceres_data/7stf_25427/03_2026/7stf_25427.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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7stf_25427/03_2026/7stf_25427.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7stf_25427/03_2026/7stf_25427.map" model { file = "/net/cci-nas-00/data/ceres_data/7stf_25427/03_2026/7stf_25427.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7stf_25427/03_2026/7stf_25427.cif" } 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= 0.000 sd= 0.001 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: 4 Type Number sf(0) Gaussians S 23 5.16 5 C 4030 2.51 5 N 1104 2.21 5 O 1257 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 43 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 6414 Number of models: 1 Model: "" Number of chains: 5 Chain: "H" Number of atoms: 1599 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1599 Classifications: {'peptide': 216} Link IDs: {'PTRANS': 13, 'TRANS': 202} Chain breaks: 1 Chain: "C" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 62 Classifications: {'peptide': 10} Modifications used: {'COO': 1} Link IDs: {'TRANS': 9} Chain: "L" Number of atoms: 1663 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1663 Classifications: {'peptide': 214} Link IDs: {'PTRANS': 11, 'TRANS': 202} Chain: "A" Number of atoms: 2247 Number of conformers: 1 Conformer: "" Number of residues, atoms: 276, 2247 Classifications: {'peptide': 276} Link IDs: {'PTRANS': 13, 'TRANS': 262} Chain: "B" Number of atoms: 843 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 843 Classifications: {'peptide': 101} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 95} Time building chain proxies: 1.35, per 1000 atoms: 0.21 Number of scatterers: 6414 At special positions: 0 Unit cell: (70.052, 64.144, 145.168, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 23 16.00 O 1257 8.00 N 1104 7.00 C 4030 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.05 Simple disulfide: pdb=" SG CYS H 148 " - pdb=" SG CYS H 204 " distance=2.04 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS L 136 " - pdb=" SG CYS L 196 " distance=2.04 Simple disulfide: pdb=" SG CYS A 101 " - pdb=" SG CYS A 164 " distance=2.03 Simple disulfide: pdb=" SG CYS A 203 " - pdb=" SG CYS A 259 " distance=2.04 Simple disulfide: pdb=" SG CYS B 45 " - pdb=" SG CYS B 100 " distance=2.03 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: 0.50 Conformation dependent library (CDL) restraints added in 307.8 milliseconds 1610 Ramachandran restraints generated. 805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1520 Finding SS restraints... Secondary structure from input PDB file: 10 helices and 16 sheets defined 12.5% alpha, 19.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.13 Creating SS restraints... Processing helix chain 'H' and resid 193 through 200 Processing helix chain 'L' and resid 124 through 129 removed outlier: 3.652A pdb=" N LYS L 128 " --> pdb=" O ASP L 124 " (cutoff:3.500A) Processing helix chain 'L' and resid 184 through 191 removed outlier: 3.861A pdb=" N TYR L 188 " --> pdb=" O SER L 184 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N HIS L 191 " --> pdb=" O ASP L 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 49 through 55 removed outlier: 4.616A pdb=" N GLN A 54 " --> pdb=" O TRP A 51 " (cutoff:3.500A) Processing helix chain 'A' and resid 56 through 78 Processing helix chain 'A' and resid 80 through 85 Processing helix chain 'A' and resid 139 through 149 Processing helix chain 'A' and resid 151 through 175 Processing helix chain 'A' and resid 225 through 228 removed outlier: 3.633A pdb=" N THR A 228 " --> pdb=" O THR A 225 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 225 through 228' Processing helix chain 'A' and resid 252 through 255 removed outlier: 3.654A pdb=" N GLN A 255 " --> pdb=" O GLY A 252 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 252 through 255' Processing sheet with id=AA1, first strand: chain 'H' and resid 45 through 46 removed outlier: 3.567A pdb=" N GLN H 39 " --> pdb=" O VAL H 93 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'H' and resid 127 through 131 removed outlier: 4.749A pdb=" N LYS H 151 " --> pdb=" O LEU H 186 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N LEU H 186 " --> pdb=" O LYS H 151 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 127 through 131 Processing sheet with id=AA4, first strand: chain 'H' and resid 159 through 162 removed outlier: 3.865A pdb=" N TYR H 202 " --> pdb=" O VAL H 219 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'L' and resid 19 through 22 removed outlier: 3.786A pdb=" N THR L 74 " --> pdb=" O SER L 65 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'L' and resid 44 through 46 Processing sheet with id=AA7, first strand: chain 'L' and resid 116 through 120 removed outlier: 3.910A pdb=" N PHE L 118 " --> pdb=" O LEU L 137 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N LEU L 137 " --> pdb=" O PHE L 118 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N PHE L 120 " --> pdb=" O VAL L 135 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N VAL L 135 " --> pdb=" O PHE L 120 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'L' and resid 147 through 148 removed outlier: 3.755A pdb=" N THR L 199 " --> pdb=" O LYS L 147 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'L' and resid 168 through 169 Processing sheet with id=AB1, first strand: chain 'A' and resid 6 through 10 removed outlier: 6.959A pdb=" N GLY A 26 " --> pdb=" O PHE A 33 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 96 through 97 Processing sheet with id=AB3, first strand: chain 'A' and resid 186 through 192 Processing sheet with id=AB4, first strand: chain 'A' and resid 186 through 192 Processing sheet with id=AB5, first strand: chain 'A' and resid 222 through 223 removed outlier: 3.624A pdb=" N THR A 214 " --> pdb=" O GLN A 262 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 29 through 31 removed outlier: 3.777A pdb=" N PHE B 90 " --> pdb=" O ASN B 41 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 60 through 61 removed outlier: 3.713A pdb=" N GLU B 64 " --> pdb=" O LYS B 61 " (cutoff:3.500A) 167 hydrogen bonds defined for protein. 417 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.77 Time building geometry restraints manager: 0.65 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 2076 1.34 - 1.47: 1710 1.47 - 1.59: 2755 1.59 - 1.72: 0 1.72 - 1.85: 32 Bond restraints: 6573 Sorted by residual: bond pdb=" C ARG H 98 " pdb=" N ALA H 99 " ideal model delta sigma weight residual 1.335 1.275 0.060 1.97e-02 2.58e+03 9.41e+00 bond pdb=" CB GLN L 89 " pdb=" CG GLN L 89 " ideal model delta sigma weight residual 1.520 1.435 0.085 3.00e-02 1.11e+03 8.06e+00 bond pdb=" CA TYR L 55 " pdb=" CB TYR L 55 " ideal model delta sigma weight residual 1.534 1.488 0.045 1.72e-02 3.38e+03 6.94e+00 bond pdb=" CG ARG H 98 " pdb=" CD ARG H 98 " ideal model delta sigma weight residual 1.520 1.448 0.072 3.00e-02 1.11e+03 5.80e+00 bond pdb=" N PHE L 53 " pdb=" CA PHE L 53 " ideal model delta sigma weight residual 1.463 1.433 0.030 1.27e-02 6.20e+03 5.53e+00 ... (remaining 6568 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.09: 8668 3.09 - 6.18: 230 6.18 - 9.26: 31 9.26 - 12.35: 4 12.35 - 15.44: 2 Bond angle restraints: 8935 Sorted by residual: angle pdb=" C PHE B 50 " pdb=" N HIS B 51 " pdb=" CA HIS B 51 " ideal model delta sigma weight residual 121.80 106.36 15.44 2.44e+00 1.68e-01 4.00e+01 angle pdb=" C SER L 52 " pdb=" N PHE L 53 " pdb=" CA PHE L 53 " ideal model delta sigma weight residual 121.72 131.19 -9.47 1.54e+00 4.22e-01 3.78e+01 angle pdb=" C GLN L 90 " pdb=" N SER L 91 " pdb=" CA SER L 91 " ideal model delta sigma weight residual 121.54 132.85 -11.31 1.91e+00 2.74e-01 3.51e+01 angle pdb=" C ILE L 48 " pdb=" N TYR L 49 " pdb=" CA TYR L 49 " ideal model delta sigma weight residual 122.42 113.90 8.52 1.55e+00 4.16e-01 3.02e+01 angle pdb=" N TYR L 92 " pdb=" CA TYR L 92 " pdb=" C TYR L 92 " ideal model delta sigma weight residual 110.80 122.19 -11.39 2.13e+00 2.20e-01 2.86e+01 ... (remaining 8930 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.18: 3403 16.18 - 32.36: 405 32.36 - 48.53: 79 48.53 - 64.71: 15 64.71 - 80.89: 15 Dihedral angle restraints: 3917 sinusoidal: 1545 harmonic: 2372 Sorted by residual: dihedral pdb=" CA SER L 91 " pdb=" C SER L 91 " pdb=" N TYR L 92 " pdb=" CA TYR L 92 " ideal model delta harmonic sigma weight residual -180.00 -124.10 -55.90 0 5.00e+00 4.00e-02 1.25e+02 dihedral pdb=" CA ASP A 29 " pdb=" C ASP A 29 " pdb=" N ASP A 30 " pdb=" CA ASP A 30 " ideal model delta harmonic sigma weight residual 180.00 134.30 45.70 0 5.00e+00 4.00e-02 8.35e+01 dihedral pdb=" CA ASN H 77 " pdb=" C ASN H 77 " pdb=" N THR H 78 " pdb=" CA THR H 78 " ideal model delta harmonic sigma weight residual -180.00 -140.14 -39.86 0 5.00e+00 4.00e-02 6.36e+01 ... (remaining 3914 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.105: 882 0.105 - 0.209: 82 0.209 - 0.314: 1 0.314 - 0.418: 1 0.418 - 0.523: 1 Chirality restraints: 967 Sorted by residual: chirality pdb=" CG LEU L 46 " pdb=" CB LEU L 46 " pdb=" CD1 LEU L 46 " pdb=" CD2 LEU L 46 " both_signs ideal model delta sigma weight residual False -2.59 -2.07 -0.52 2.00e-01 2.50e+01 6.84e+00 chirality pdb=" CG LEU L 73 " pdb=" CB LEU L 73 " pdb=" CD1 LEU L 73 " pdb=" CD2 LEU L 73 " both_signs ideal model delta sigma weight residual False -2.59 -2.24 -0.35 2.00e-01 2.50e+01 3.09e+00 chirality pdb=" CA MET H 52 " pdb=" N MET H 52 " pdb=" C MET H 52 " pdb=" CB MET H 52 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.74e+00 ... (remaining 964 not shown) Planarity restraints: 1161 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY H 125 " -0.061 5.00e-02 4.00e+02 9.25e-02 1.37e+01 pdb=" N PRO H 126 " 0.160 5.00e-02 4.00e+02 pdb=" CA PRO H 126 " -0.049 5.00e-02 4.00e+02 pdb=" CD PRO H 126 " -0.050 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 160 " 0.018 2.00e-02 2.50e+03 3.63e-02 1.32e+01 pdb=" C LEU A 160 " -0.063 2.00e-02 2.50e+03 pdb=" O LEU A 160 " 0.023 2.00e-02 2.50e+03 pdb=" N ASP A 161 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR H 109 " 0.031 2.00e-02 2.50e+03 2.12e-02 8.98e+00 pdb=" CG TYR H 109 " -0.050 2.00e-02 2.50e+03 pdb=" CD1 TYR H 109 " 0.004 2.00e-02 2.50e+03 pdb=" CD2 TYR H 109 " 0.000 2.00e-02 2.50e+03 pdb=" CE1 TYR H 109 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR H 109 " 0.005 2.00e-02 2.50e+03 pdb=" CZ TYR H 109 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR H 109 " 0.006 2.00e-02 2.50e+03 ... (remaining 1158 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.58: 134 2.58 - 3.16: 6039 3.16 - 3.74: 10420 3.74 - 4.32: 14730 4.32 - 4.90: 23459 Nonbonded interactions: 54782 Sorted by model distance: nonbonded pdb=" NH1 ARG L 24 " pdb=" O ASP L 70 " model vdw 1.998 3.120 nonbonded pdb=" OG SER B 31 " pdb=" O HIS B 33 " model vdw 2.054 3.040 nonbonded pdb=" O HIS H 208 " pdb=" OG SER H 211 " model vdw 2.115 3.040 nonbonded pdb=" OG SER H 75 " pdb=" OD1 ASN H 77 " model vdw 2.120 3.040 nonbonded pdb=" O VAL H 2 " pdb=" ND2 ASN H 101 " model vdw 2.164 3.120 ... (remaining 54777 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.700 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: 0.000 Extract box with map and model: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 6.440 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6891 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 : 0.009 0.085 6580 Z= 0.404 Angle : 1.209 15.438 8949 Z= 0.665 Chirality : 0.062 0.523 967 Planarity : 0.007 0.093 1161 Dihedral : 15.262 80.889 2376 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 37.36 Ramachandran Plot: Outliers : 0.75 % Allowed : 20.12 % Favored : 79.13 % Rotamer: Outliers : 0.14 % Allowed : 0.85 % Favored : 99.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.76 % Twisted General : 1.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.76 (0.27), residues: 805 helix: -1.22 (0.53), residues: 87 sheet: -1.69 (0.34), residues: 211 loop : -3.30 (0.25), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 82 TYR 0.050 0.005 TYR H 109 PHE 0.044 0.004 PHE L 95 TRP 0.018 0.003 TRP H 162 HIS 0.012 0.003 HIS H 57 Details of bonding type rmsd covalent geometry : bond 0.00889 ( 6573) covalent geometry : angle 1.20649 ( 8935) SS BOND : bond 0.01004 ( 7) SS BOND : angle 2.13854 ( 14) hydrogen bonds : bond 0.28533 ( 145) hydrogen bonds : angle 10.69457 ( 417) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1610 Ramachandran restraints generated. 805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1610 Ramachandran restraints generated. 805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 97 time to evaluate : 0.282 Fit side-chains revert: symmetry clash REVERT: H 35 HIS cc_start: 0.7543 (m170) cc_final: 0.7150 (m-70) REVERT: B 39 LYS cc_start: 0.7565 (mmtm) cc_final: 0.7345 (mptt) outliers start: 1 outliers final: 0 residues processed: 98 average time/residue: 0.1003 time to fit residues: 12.3992 Evaluate side-chains 72 residues out of total 703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 72 time to evaluate : 0.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 49 optimal weight: 0.6980 chunk 53 optimal weight: 0.7980 chunk 5 optimal weight: 0.7980 chunk 33 optimal weight: 0.5980 chunk 65 optimal weight: 7.9990 chunk 62 optimal weight: 7.9990 chunk 51 optimal weight: 0.7980 chunk 38 optimal weight: 0.9990 chunk 61 optimal weight: 8.9990 chunk 45 optimal weight: 0.7980 chunk 74 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 32 GLN ** A 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 41 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4538 r_free = 0.4538 target = 0.141647 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.107786 restraints weight = 13594.553| |-----------------------------------------------------------------------------| r_work (start): 0.4020 rms_B_bonded: 3.10 r_work: 0.3893 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3893 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7000 moved from start: 0.1963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 6580 Z= 0.178 Angle : 0.905 10.583 8949 Z= 0.480 Chirality : 0.050 0.196 967 Planarity : 0.006 0.059 1161 Dihedral : 8.409 70.023 896 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 21.51 Ramachandran Plot: Outliers : 0.25 % Allowed : 15.03 % Favored : 84.72 % Rotamer: Outliers : 0.85 % Allowed : 10.10 % Favored : 89.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.38 % Twisted General : 0.65 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.53 (0.28), residues: 805 helix: -0.62 (0.55), residues: 97 sheet: -1.56 (0.34), residues: 220 loop : -3.27 (0.26), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG L 24 TYR 0.023 0.002 TYR L 175 PHE 0.030 0.002 PHE L 95 TRP 0.030 0.002 TRP A 204 HIS 0.011 0.002 HIS B 51 Details of bonding type rmsd covalent geometry : bond 0.00396 ( 6573) covalent geometry : angle 0.90397 ( 8935) SS BOND : bond 0.00505 ( 7) SS BOND : angle 1.24689 ( 14) hydrogen bonds : bond 0.04875 ( 145) hydrogen bonds : angle 7.28115 ( 417) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1610 Ramachandran restraints generated. 805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1610 Ramachandran restraints generated. 805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 92 time to evaluate : 0.263 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 73 ASP cc_start: 0.7142 (p0) cc_final: 0.6438 (m-30) REVERT: H 98 ARG cc_start: 0.6961 (tpp-160) cc_final: 0.6595 (mtt-85) REVERT: H 110 TRP cc_start: 0.5085 (p90) cc_final: 0.4287 (p90) REVERT: H 153 TYR cc_start: 0.6328 (p90) cc_final: 0.5547 (p90) REVERT: H 163 ASN cc_start: 0.7270 (t0) cc_final: 0.6979 (m-40) REVERT: L 55 TYR cc_start: 0.6234 (t80) cc_final: 0.6008 (t80) REVERT: A 108 ARG cc_start: 0.7192 (tpt170) cc_final: 0.6954 (tpt170) REVERT: B 36 GLU cc_start: 0.6642 (tp30) cc_final: 0.6289 (tp30) REVERT: B 37 ASN cc_start: 0.7888 (m110) cc_final: 0.7430 (m-40) REVERT: B 118 ASP cc_start: 0.7879 (t0) cc_final: 0.7665 (t0) outliers start: 6 outliers final: 6 residues processed: 95 average time/residue: 0.0826 time to fit residues: 10.2663 Evaluate side-chains 79 residues out of total 703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 73 time to evaluate : 0.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 80 TYR Chi-restraints excluded: chain H residue 116 VAL Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain L residue 108 ILE Chi-restraints excluded: chain A residue 93 HIS Chi-restraints excluded: chain B residue 40 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 12 optimal weight: 6.9990 chunk 21 optimal weight: 1.9990 chunk 15 optimal weight: 10.0000 chunk 67 optimal weight: 6.9990 chunk 34 optimal weight: 8.9990 chunk 33 optimal weight: 1.9990 chunk 1 optimal weight: 0.3980 chunk 49 optimal weight: 0.8980 chunk 50 optimal weight: 0.9990 chunk 25 optimal weight: 1.9990 chunk 3 optimal weight: 0.7980 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 39 GLN ** A 93 HIS ** 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 = 0.4527 r_free = 0.4527 target = 0.140327 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.106384 restraints weight = 13452.341| |-----------------------------------------------------------------------------| r_work (start): 0.3995 rms_B_bonded: 3.00 r_work: 0.3868 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3868 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7041 moved from start: 0.2416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 6580 Z= 0.187 Angle : 0.852 10.701 8949 Z= 0.451 Chirality : 0.049 0.213 967 Planarity : 0.006 0.059 1161 Dihedral : 8.017 65.869 896 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 21.51 Ramachandran Plot: Outliers : 0.25 % Allowed : 16.02 % Favored : 83.73 % Rotamer: Outliers : 2.56 % Allowed : 13.94 % Favored : 83.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.65 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.47 (0.28), residues: 805 helix: -0.53 (0.55), residues: 96 sheet: -1.52 (0.34), residues: 215 loop : -3.22 (0.26), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG L 61 TYR 0.025 0.002 TYR L 49 PHE 0.013 0.002 PHE H 129 TRP 0.019 0.002 TRP A 204 HIS 0.009 0.001 HIS B 51 Details of bonding type rmsd covalent geometry : bond 0.00426 ( 6573) covalent geometry : angle 0.85120 ( 8935) SS BOND : bond 0.00697 ( 7) SS BOND : angle 1.34528 ( 14) hydrogen bonds : bond 0.04424 ( 145) hydrogen bonds : angle 6.87112 ( 417) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1610 Ramachandran restraints generated. 805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1610 Ramachandran restraints generated. 805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 77 time to evaluate : 0.239 Fit side-chains REVERT: H 31 TYR cc_start: 0.6340 (OUTLIER) cc_final: 0.5660 (t80) REVERT: H 73 ASP cc_start: 0.7205 (p0) cc_final: 0.6537 (m-30) REVERT: H 110 TRP cc_start: 0.4799 (p90) cc_final: 0.4417 (p90) REVERT: H 153 TYR cc_start: 0.6491 (p90) cc_final: 0.5657 (p90) REVERT: H 163 ASN cc_start: 0.7017 (t0) cc_final: 0.6737 (m-40) REVERT: B 36 GLU cc_start: 0.6674 (tp30) cc_final: 0.6426 (tp30) REVERT: B 37 ASN cc_start: 0.7869 (m110) cc_final: 0.7407 (m-40) REVERT: B 116 ASP cc_start: 0.8267 (t0) cc_final: 0.7995 (t0) outliers start: 18 outliers final: 11 residues processed: 88 average time/residue: 0.0819 time to fit residues: 9.5549 Evaluate side-chains 79 residues out of total 703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 67 time to evaluate : 0.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 31 TYR Chi-restraints excluded: chain H residue 116 VAL Chi-restraints excluded: chain H residue 148 CYS Chi-restraints excluded: chain H residue 202 TYR Chi-restraints excluded: chain L residue 50 SER Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain L residue 108 ILE Chi-restraints excluded: chain L residue 127 LEU Chi-restraints excluded: chain A residue 5 MET Chi-restraints excluded: chain A residue 93 HIS Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain B residue 40 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 2 optimal weight: 3.9990 chunk 52 optimal weight: 0.8980 chunk 4 optimal weight: 0.5980 chunk 36 optimal weight: 5.9990 chunk 75 optimal weight: 0.9990 chunk 58 optimal weight: 3.9990 chunk 53 optimal weight: 0.0060 chunk 30 optimal weight: 2.9990 chunk 16 optimal weight: 0.7980 chunk 14 optimal weight: 4.9990 chunk 31 optimal weight: 0.9990 overall best weight: 0.6598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 41 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4557 r_free = 0.4557 target = 0.142505 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.108572 restraints weight = 13516.435| |-----------------------------------------------------------------------------| r_work (start): 0.4034 rms_B_bonded: 3.05 r_work: 0.3908 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3908 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6968 moved from start: 0.2873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 6580 Z= 0.156 Angle : 0.811 10.605 8949 Z= 0.426 Chirality : 0.047 0.209 967 Planarity : 0.006 0.056 1161 Dihedral : 7.654 61.235 896 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 18.48 Ramachandran Plot: Outliers : 0.25 % Allowed : 14.66 % Favored : 85.09 % Rotamer: Outliers : 3.13 % Allowed : 14.94 % Favored : 81.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.39 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.31 (0.28), residues: 805 helix: -0.41 (0.55), residues: 95 sheet: -1.53 (0.35), residues: 219 loop : -3.06 (0.26), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG L 61 TYR 0.018 0.002 TYR L 49 PHE 0.014 0.002 PHE H 129 TRP 0.020 0.002 TRP A 204 HIS 0.008 0.001 HIS B 51 Details of bonding type rmsd covalent geometry : bond 0.00359 ( 6573) covalent geometry : angle 0.80983 ( 8935) SS BOND : bond 0.00554 ( 7) SS BOND : angle 1.27967 ( 14) hydrogen bonds : bond 0.03919 ( 145) hydrogen bonds : angle 6.59671 ( 417) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1610 Ramachandran restraints generated. 805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1610 Ramachandran restraints generated. 805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 79 time to evaluate : 0.187 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 31 TYR cc_start: 0.6137 (OUTLIER) cc_final: 0.5544 (t80) REVERT: H 73 ASP cc_start: 0.7107 (p0) cc_final: 0.6538 (m-30) REVERT: H 153 TYR cc_start: 0.6542 (p90) cc_final: 0.5718 (p90) REVERT: H 163 ASN cc_start: 0.7077 (t0) cc_final: 0.6834 (m-40) REVERT: L 141 PHE cc_start: 0.6250 (p90) cc_final: 0.6029 (p90) REVERT: A 108 ARG cc_start: 0.7198 (tpt170) cc_final: 0.6894 (tpt170) REVERT: B 36 GLU cc_start: 0.6726 (tp30) cc_final: 0.6472 (tp30) REVERT: B 37 ASN cc_start: 0.7838 (m110) cc_final: 0.7401 (m-40) REVERT: B 112 ILE cc_start: 0.8670 (OUTLIER) cc_final: 0.8442 (mp) REVERT: B 116 ASP cc_start: 0.8280 (t0) cc_final: 0.7946 (t0) outliers start: 22 outliers final: 17 residues processed: 95 average time/residue: 0.0794 time to fit residues: 9.9710 Evaluate side-chains 88 residues out of total 703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 69 time to evaluate : 0.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 6 GLU Chi-restraints excluded: chain H residue 31 TYR Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 116 VAL Chi-restraints excluded: chain H residue 148 CYS Chi-restraints excluded: chain H residue 202 TYR Chi-restraints excluded: chain H residue 215 VAL Chi-restraints excluded: chain L residue 50 SER Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain L residue 108 ILE Chi-restraints excluded: chain L residue 127 LEU Chi-restraints excluded: chain L residue 198 VAL Chi-restraints excluded: chain A residue 5 MET Chi-restraints excluded: chain A residue 93 HIS Chi-restraints excluded: chain A residue 214 THR Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain B residue 40 SER Chi-restraints excluded: chain B residue 112 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 26 optimal weight: 0.1980 chunk 70 optimal weight: 1.9990 chunk 8 optimal weight: 4.9990 chunk 10 optimal weight: 0.8980 chunk 58 optimal weight: 3.9990 chunk 60 optimal weight: 0.9990 chunk 67 optimal weight: 2.9990 chunk 13 optimal weight: 20.0000 chunk 73 optimal weight: 1.9990 chunk 72 optimal weight: 0.7980 chunk 48 optimal weight: 0.9980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 226 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 = 0.4555 r_free = 0.4555 target = 0.142394 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.107902 restraints weight = 13513.697| |-----------------------------------------------------------------------------| r_work (start): 0.4022 rms_B_bonded: 3.13 r_work: 0.3896 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3896 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6983 moved from start: 0.3233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 6580 Z= 0.156 Angle : 0.784 10.304 8949 Z= 0.411 Chirality : 0.047 0.204 967 Planarity : 0.006 0.086 1161 Dihedral : 7.400 55.338 896 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 17.84 Ramachandran Plot: Outliers : 0.25 % Allowed : 15.16 % Favored : 84.60 % Rotamer: Outliers : 3.41 % Allowed : 16.79 % Favored : 79.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.39 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.41 (0.28), residues: 805 helix: -0.45 (0.53), residues: 101 sheet: -1.56 (0.34), residues: 227 loop : -3.21 (0.26), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG H 98 TYR 0.022 0.002 TYR A 84 PHE 0.014 0.002 PHE H 129 TRP 0.015 0.002 TRP A 204 HIS 0.008 0.001 HIS B 51 Details of bonding type rmsd covalent geometry : bond 0.00359 ( 6573) covalent geometry : angle 0.78339 ( 8935) SS BOND : bond 0.00647 ( 7) SS BOND : angle 1.24795 ( 14) hydrogen bonds : bond 0.03778 ( 145) hydrogen bonds : angle 6.41098 ( 417) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1610 Ramachandran restraints generated. 805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1610 Ramachandran restraints generated. 805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 75 time to evaluate : 0.240 Fit side-chains revert: symmetry clash REVERT: H 31 TYR cc_start: 0.6047 (OUTLIER) cc_final: 0.5499 (t80) REVERT: H 73 ASP cc_start: 0.7125 (p0) cc_final: 0.6618 (m-30) REVERT: H 98 ARG cc_start: 0.5883 (mtm110) cc_final: 0.5637 (mtm180) REVERT: H 153 TYR cc_start: 0.6619 (p90) cc_final: 0.5805 (p90) REVERT: H 163 ASN cc_start: 0.7059 (t0) cc_final: 0.6815 (m-40) REVERT: L 141 PHE cc_start: 0.6178 (p90) cc_final: 0.5969 (p90) REVERT: A 204 TRP cc_start: 0.7386 (m100) cc_final: 0.7170 (m100) REVERT: B 37 ASN cc_start: 0.7864 (m110) cc_final: 0.7421 (m-40) REVERT: B 112 ILE cc_start: 0.8692 (OUTLIER) cc_final: 0.8480 (mp) REVERT: B 116 ASP cc_start: 0.8316 (t0) cc_final: 0.7961 (t0) outliers start: 24 outliers final: 16 residues processed: 93 average time/residue: 0.0798 time to fit residues: 9.9578 Evaluate side-chains 86 residues out of total 703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 68 time to evaluate : 0.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 31 TYR Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 80 TYR Chi-restraints excluded: chain H residue 116 VAL Chi-restraints excluded: chain H residue 148 CYS Chi-restraints excluded: chain H residue 202 TYR Chi-restraints excluded: chain H residue 215 VAL Chi-restraints excluded: chain L residue 50 SER Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain L residue 108 ILE Chi-restraints excluded: chain L residue 127 LEU Chi-restraints excluded: chain L residue 198 VAL Chi-restraints excluded: chain A residue 5 MET Chi-restraints excluded: chain A residue 93 HIS Chi-restraints excluded: chain A residue 214 THR Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain B residue 40 SER Chi-restraints excluded: chain B residue 112 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 67 optimal weight: 1.9990 chunk 59 optimal weight: 3.9990 chunk 70 optimal weight: 1.9990 chunk 41 optimal weight: 9.9990 chunk 50 optimal weight: 0.9990 chunk 58 optimal weight: 2.9990 chunk 36 optimal weight: 3.9990 chunk 13 optimal weight: 20.0000 chunk 5 optimal weight: 0.0270 chunk 3 optimal weight: 0.6980 chunk 78 optimal weight: 2.9990 overall best weight: 1.1444 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 139 ASN ** A 226 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 = 0.4536 r_free = 0.4536 target = 0.141339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.106783 restraints weight = 13493.349| |-----------------------------------------------------------------------------| r_work (start): 0.3997 rms_B_bonded: 3.06 r_work: 0.3872 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3872 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7032 moved from start: 0.3264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 6580 Z= 0.183 Angle : 0.814 10.366 8949 Z= 0.424 Chirality : 0.048 0.212 967 Planarity : 0.006 0.061 1161 Dihedral : 7.408 57.592 896 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 19.35 Ramachandran Plot: Outliers : 0.25 % Allowed : 15.90 % Favored : 83.85 % Rotamer: Outliers : 3.27 % Allowed : 17.92 % Favored : 78.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.39 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.42 (0.28), residues: 805 helix: -0.43 (0.54), residues: 100 sheet: -1.51 (0.35), residues: 214 loop : -3.22 (0.25), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 98 TYR 0.023 0.002 TYR L 49 PHE 0.014 0.002 PHE H 129 TRP 0.013 0.002 TRP H 36 HIS 0.008 0.001 HIS B 51 Details of bonding type rmsd covalent geometry : bond 0.00420 ( 6573) covalent geometry : angle 0.81263 ( 8935) SS BOND : bond 0.00524 ( 7) SS BOND : angle 1.38317 ( 14) hydrogen bonds : bond 0.03856 ( 145) hydrogen bonds : angle 6.35007 ( 417) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1610 Ramachandran restraints generated. 805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1610 Ramachandran restraints generated. 805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 75 time to evaluate : 0.226 Fit side-chains revert: symmetry clash REVERT: H 31 TYR cc_start: 0.6114 (OUTLIER) cc_final: 0.5419 (t80) REVERT: H 73 ASP cc_start: 0.7327 (p0) cc_final: 0.6732 (m-30) REVERT: H 105 TYR cc_start: 0.7525 (OUTLIER) cc_final: 0.5985 (t80) REVERT: H 153 TYR cc_start: 0.6612 (p90) cc_final: 0.5718 (p90) REVERT: A 108 ARG cc_start: 0.7129 (tpt170) cc_final: 0.6824 (tpt170) REVERT: A 204 TRP cc_start: 0.7509 (m100) cc_final: 0.7272 (m100) REVERT: B 36 GLU cc_start: 0.6147 (tp30) cc_final: 0.5505 (tp30) REVERT: B 39 LYS cc_start: 0.8364 (mmtm) cc_final: 0.7923 (mmtm) REVERT: B 112 ILE cc_start: 0.8712 (OUTLIER) cc_final: 0.8501 (mp) REVERT: B 116 ASP cc_start: 0.8386 (t0) cc_final: 0.8033 (t0) outliers start: 23 outliers final: 16 residues processed: 91 average time/residue: 0.0739 time to fit residues: 9.0785 Evaluate side-chains 90 residues out of total 703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 71 time to evaluate : 0.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 31 TYR Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 80 TYR Chi-restraints excluded: chain H residue 105 TYR Chi-restraints excluded: chain H residue 116 VAL Chi-restraints excluded: chain H residue 202 TYR Chi-restraints excluded: chain H residue 215 VAL Chi-restraints excluded: chain L residue 50 SER Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain L residue 108 ILE Chi-restraints excluded: chain L residue 127 LEU Chi-restraints excluded: chain L residue 198 VAL Chi-restraints excluded: chain A residue 5 MET Chi-restraints excluded: chain A residue 93 HIS Chi-restraints excluded: chain A residue 214 THR Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain B residue 40 SER Chi-restraints excluded: chain B residue 112 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 6 optimal weight: 5.9990 chunk 33 optimal weight: 2.9990 chunk 4 optimal weight: 2.9990 chunk 0 optimal weight: 6.9990 chunk 11 optimal weight: 7.9990 chunk 14 optimal weight: 6.9990 chunk 19 optimal weight: 9.9990 chunk 12 optimal weight: 5.9990 chunk 52 optimal weight: 2.9990 chunk 5 optimal weight: 0.9980 chunk 66 optimal weight: 0.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 212 ASN ** A 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 242 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4479 r_free = 0.4479 target = 0.137175 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.102734 restraints weight = 13480.643| |-----------------------------------------------------------------------------| r_work (start): 0.3923 rms_B_bonded: 3.00 r_work: 0.3795 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3795 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7159 moved from start: 0.3117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.078 6580 Z= 0.292 Angle : 0.903 11.582 8949 Z= 0.478 Chirality : 0.051 0.266 967 Planarity : 0.007 0.108 1161 Dihedral : 7.979 63.754 896 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 24.85 Ramachandran Plot: Outliers : 0.25 % Allowed : 17.89 % Favored : 81.86 % Rotamer: Outliers : 3.84 % Allowed : 19.35 % Favored : 76.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.52 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.64 (0.27), residues: 805 helix: -0.63 (0.52), residues: 101 sheet: -1.70 (0.34), residues: 214 loop : -3.34 (0.25), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG H 98 TYR 0.037 0.004 TYR L 49 PHE 0.044 0.003 PHE L 141 TRP 0.025 0.003 TRP H 110 HIS 0.010 0.002 HIS B 51 Details of bonding type rmsd covalent geometry : bond 0.00661 ( 6573) covalent geometry : angle 0.90095 ( 8935) SS BOND : bond 0.00876 ( 7) SS BOND : angle 1.93035 ( 14) hydrogen bonds : bond 0.04414 ( 145) hydrogen bonds : angle 6.63509 ( 417) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1610 Ramachandran restraints generated. 805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1610 Ramachandran restraints generated. 805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 70 time to evaluate : 0.241 Fit side-chains REVERT: H 31 TYR cc_start: 0.6319 (OUTLIER) cc_final: 0.5452 (t80) REVERT: H 77 ASN cc_start: 0.7523 (m-40) cc_final: 0.6978 (t0) REVERT: H 105 TYR cc_start: 0.7657 (OUTLIER) cc_final: 0.6199 (t80) REVERT: H 153 TYR cc_start: 0.6723 (p90) cc_final: 0.5825 (p90) REVERT: A 108 ARG cc_start: 0.7202 (tpt170) cc_final: 0.6966 (tpt170) REVERT: A 204 TRP cc_start: 0.7728 (m100) cc_final: 0.7426 (m100) REVERT: B 36 GLU cc_start: 0.6344 (tp30) cc_final: 0.5987 (tp30) REVERT: B 116 ASP cc_start: 0.8532 (t0) cc_final: 0.8230 (t0) outliers start: 27 outliers final: 19 residues processed: 92 average time/residue: 0.0750 time to fit residues: 9.3779 Evaluate side-chains 87 residues out of total 703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 66 time to evaluate : 0.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 31 TYR Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 80 TYR Chi-restraints excluded: chain H residue 105 TYR Chi-restraints excluded: chain H residue 116 VAL Chi-restraints excluded: chain H residue 117 THR Chi-restraints excluded: chain H residue 215 VAL Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 50 SER Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain L residue 108 ILE Chi-restraints excluded: chain L residue 198 VAL Chi-restraints excluded: chain A residue 5 MET Chi-restraints excluded: chain A residue 93 HIS Chi-restraints excluded: chain A residue 188 HIS Chi-restraints excluded: chain A residue 214 THR Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain B residue 40 SER Chi-restraints excluded: chain B residue 90 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 32 optimal weight: 5.9990 chunk 53 optimal weight: 0.6980 chunk 6 optimal weight: 3.9990 chunk 11 optimal weight: 0.9990 chunk 42 optimal weight: 2.9990 chunk 69 optimal weight: 0.3980 chunk 47 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 chunk 20 optimal weight: 4.9990 chunk 44 optimal weight: 1.9990 chunk 64 optimal weight: 6.9990 overall best weight: 1.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 242 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4511 r_free = 0.4511 target = 0.139490 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.105164 restraints weight = 13333.518| |-----------------------------------------------------------------------------| r_work (start): 0.3965 rms_B_bonded: 3.02 r_work: 0.3844 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3844 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7068 moved from start: 0.3363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 6580 Z= 0.197 Angle : 0.836 10.452 8949 Z= 0.437 Chirality : 0.049 0.234 967 Planarity : 0.007 0.078 1161 Dihedral : 7.691 61.843 896 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 21.66 Ramachandran Plot: Outliers : 0.25 % Allowed : 16.27 % Favored : 83.48 % Rotamer: Outliers : 3.70 % Allowed : 19.63 % Favored : 76.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.39 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.51 (0.28), residues: 805 helix: -0.43 (0.53), residues: 100 sheet: -1.62 (0.34), residues: 213 loop : -3.26 (0.25), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG H 98 TYR 0.026 0.003 TYR L 49 PHE 0.031 0.002 PHE L 141 TRP 0.020 0.002 TRP H 110 HIS 0.009 0.001 HIS B 51 Details of bonding type rmsd covalent geometry : bond 0.00448 ( 6573) covalent geometry : angle 0.83442 ( 8935) SS BOND : bond 0.00656 ( 7) SS BOND : angle 1.50316 ( 14) hydrogen bonds : bond 0.03909 ( 145) hydrogen bonds : angle 6.43406 ( 417) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1610 Ramachandran restraints generated. 805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1610 Ramachandran restraints generated. 805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 72 time to evaluate : 0.211 Fit side-chains REVERT: H 31 TYR cc_start: 0.6004 (OUTLIER) cc_final: 0.5424 (t80) REVERT: H 35 HIS cc_start: 0.7662 (m170) cc_final: 0.7440 (m-70) REVERT: H 73 ASP cc_start: 0.7482 (p0) cc_final: 0.6701 (m-30) REVERT: H 77 ASN cc_start: 0.7398 (m-40) cc_final: 0.6930 (t0) REVERT: H 105 TYR cc_start: 0.7549 (OUTLIER) cc_final: 0.6022 (t80) REVERT: H 107 PHE cc_start: 0.8238 (m-80) cc_final: 0.7990 (m-80) REVERT: H 150 VAL cc_start: 0.9232 (OUTLIER) cc_final: 0.8706 (t) REVERT: H 153 TYR cc_start: 0.6701 (p90) cc_final: 0.5679 (p90) REVERT: A 204 TRP cc_start: 0.7624 (m100) cc_final: 0.7307 (m100) REVERT: B 36 GLU cc_start: 0.6338 (tp30) cc_final: 0.5974 (tp30) REVERT: B 39 LYS cc_start: 0.8216 (mmtm) cc_final: 0.7837 (mmtm) REVERT: B 116 ASP cc_start: 0.8463 (t0) cc_final: 0.8142 (t0) outliers start: 26 outliers final: 21 residues processed: 93 average time/residue: 0.0747 time to fit residues: 9.5176 Evaluate side-chains 93 residues out of total 703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 69 time to evaluate : 0.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 31 TYR Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 80 TYR Chi-restraints excluded: chain H residue 105 TYR Chi-restraints excluded: chain H residue 116 VAL Chi-restraints excluded: chain H residue 150 VAL Chi-restraints excluded: chain H residue 192 VAL Chi-restraints excluded: chain H residue 202 TYR Chi-restraints excluded: chain H residue 215 VAL Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 50 SER Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain L residue 108 ILE Chi-restraints excluded: chain L residue 198 VAL Chi-restraints excluded: chain A residue 5 MET Chi-restraints excluded: chain A residue 93 HIS Chi-restraints excluded: chain A residue 138 MET Chi-restraints excluded: chain A residue 188 HIS Chi-restraints excluded: chain A residue 214 THR Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain B residue 40 SER Chi-restraints excluded: chain B residue 90 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 7 optimal weight: 0.0970 chunk 2 optimal weight: 1.9990 chunk 42 optimal weight: 0.8980 chunk 48 optimal weight: 0.7980 chunk 18 optimal weight: 7.9990 chunk 45 optimal weight: 1.9990 chunk 79 optimal weight: 0.8980 chunk 33 optimal weight: 5.9990 chunk 65 optimal weight: 1.9990 chunk 60 optimal weight: 0.5980 chunk 19 optimal weight: 8.9990 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 242 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4547 r_free = 0.4547 target = 0.141482 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.108134 restraints weight = 13697.042| |-----------------------------------------------------------------------------| r_work (start): 0.4023 rms_B_bonded: 3.03 r_work: 0.3896 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3896 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6981 moved from start: 0.3793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 6580 Z= 0.154 Angle : 0.804 10.008 8949 Z= 0.417 Chirality : 0.048 0.242 967 Planarity : 0.006 0.076 1161 Dihedral : 7.355 55.417 896 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 18.56 Ramachandran Plot: Outliers : 0.25 % Allowed : 14.91 % Favored : 84.84 % Rotamer: Outliers : 3.13 % Allowed : 20.77 % Favored : 76.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.39 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.46 (0.28), residues: 805 helix: -0.29 (0.55), residues: 100 sheet: -1.68 (0.34), residues: 219 loop : -3.22 (0.25), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG L 24 TYR 0.025 0.002 TYR A 84 PHE 0.029 0.002 PHE L 141 TRP 0.029 0.002 TRP H 110 HIS 0.009 0.001 HIS B 51 Details of bonding type rmsd covalent geometry : bond 0.00349 ( 6573) covalent geometry : angle 0.80415 ( 8935) SS BOND : bond 0.00473 ( 7) SS BOND : angle 0.97604 ( 14) hydrogen bonds : bond 0.03618 ( 145) hydrogen bonds : angle 6.24098 ( 417) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1610 Ramachandran restraints generated. 805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1610 Ramachandran restraints generated. 805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 73 time to evaluate : 0.217 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 31 TYR cc_start: 0.5823 (OUTLIER) cc_final: 0.5354 (t80) REVERT: H 35 HIS cc_start: 0.7612 (m170) cc_final: 0.7321 (m90) REVERT: H 73 ASP cc_start: 0.7173 (p0) cc_final: 0.6575 (m-30) REVERT: H 105 TYR cc_start: 0.7480 (OUTLIER) cc_final: 0.5887 (t80) REVERT: H 150 VAL cc_start: 0.9233 (OUTLIER) cc_final: 0.8710 (t) REVERT: H 153 TYR cc_start: 0.6745 (p90) cc_final: 0.5744 (p90) REVERT: L 120 PHE cc_start: 0.5561 (m-80) cc_final: 0.4951 (m-80) REVERT: A 204 TRP cc_start: 0.7540 (m100) cc_final: 0.7221 (m100) REVERT: B 36 GLU cc_start: 0.6231 (tp30) cc_final: 0.5906 (tp30) REVERT: B 39 LYS cc_start: 0.8140 (mmtm) cc_final: 0.7758 (mmtm) REVERT: B 116 ASP cc_start: 0.8413 (t0) cc_final: 0.8072 (t0) outliers start: 22 outliers final: 18 residues processed: 90 average time/residue: 0.0670 time to fit residues: 8.2558 Evaluate side-chains 93 residues out of total 703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 72 time to evaluate : 0.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 31 TYR Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 105 TYR Chi-restraints excluded: chain H residue 116 VAL Chi-restraints excluded: chain H residue 150 VAL Chi-restraints excluded: chain H residue 192 VAL Chi-restraints excluded: chain H residue 202 TYR Chi-restraints excluded: chain H residue 215 VAL Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 50 SER Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain L residue 108 ILE Chi-restraints excluded: chain L residue 198 VAL Chi-restraints excluded: chain A residue 5 MET Chi-restraints excluded: chain A residue 93 HIS Chi-restraints excluded: chain A residue 214 THR Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain B residue 40 SER Chi-restraints excluded: chain B residue 90 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 9 optimal weight: 0.9980 chunk 32 optimal weight: 0.8980 chunk 46 optimal weight: 0.4980 chunk 14 optimal weight: 5.9990 chunk 33 optimal weight: 9.9990 chunk 4 optimal weight: 1.9990 chunk 24 optimal weight: 0.9980 chunk 71 optimal weight: 0.8980 chunk 19 optimal weight: 6.9990 chunk 73 optimal weight: 0.7980 chunk 72 optimal weight: 2.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 242 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4544 r_free = 0.4544 target = 0.142003 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.107719 restraints weight = 13364.468| |-----------------------------------------------------------------------------| r_work (start): 0.4014 rms_B_bonded: 3.02 r_work: 0.3896 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3896 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6975 moved from start: 0.3862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 6580 Z= 0.159 Angle : 0.801 10.186 8949 Z= 0.413 Chirality : 0.048 0.238 967 Planarity : 0.006 0.075 1161 Dihedral : 7.236 53.341 896 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 19.04 Ramachandran Plot: Outliers : 0.25 % Allowed : 15.16 % Favored : 84.60 % Rotamer: Outliers : 2.99 % Allowed : 20.91 % Favored : 76.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.39 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.36 (0.28), residues: 805 helix: -0.23 (0.55), residues: 100 sheet: -1.57 (0.32), residues: 248 loop : -3.24 (0.27), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG L 24 TYR 0.024 0.002 TYR L 49 PHE 0.023 0.002 PHE L 141 TRP 0.023 0.002 TRP H 47 HIS 0.009 0.001 HIS B 51 Details of bonding type rmsd covalent geometry : bond 0.00368 ( 6573) covalent geometry : angle 0.80054 ( 8935) SS BOND : bond 0.00481 ( 7) SS BOND : angle 1.05901 ( 14) hydrogen bonds : bond 0.03664 ( 145) hydrogen bonds : angle 6.09284 ( 417) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1610 Ramachandran restraints generated. 805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1610 Ramachandran restraints generated. 805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 71 time to evaluate : 0.240 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 31 TYR cc_start: 0.5946 (OUTLIER) cc_final: 0.5399 (t80) REVERT: H 73 ASP cc_start: 0.7168 (p0) cc_final: 0.6614 (m-30) REVERT: H 77 ASN cc_start: 0.7267 (m-40) cc_final: 0.6823 (t0) REVERT: H 105 TYR cc_start: 0.7381 (OUTLIER) cc_final: 0.5830 (t80) REVERT: H 153 TYR cc_start: 0.6628 (p90) cc_final: 0.5699 (p90) REVERT: L 120 PHE cc_start: 0.4652 (m-80) cc_final: 0.4282 (m-80) REVERT: L 138 LEU cc_start: 0.8073 (mm) cc_final: 0.7654 (tp) REVERT: A 108 ARG cc_start: 0.7032 (tpt170) cc_final: 0.6819 (tpt170) REVERT: A 204 TRP cc_start: 0.7538 (m100) cc_final: 0.7248 (m100) REVERT: B 36 GLU cc_start: 0.6331 (tp30) cc_final: 0.5991 (tp30) REVERT: B 39 LYS cc_start: 0.8145 (mmtm) cc_final: 0.7765 (mmtm) REVERT: B 116 ASP cc_start: 0.8390 (t0) cc_final: 0.8031 (t0) outliers start: 21 outliers final: 16 residues processed: 86 average time/residue: 0.0692 time to fit residues: 8.2128 Evaluate side-chains 88 residues out of total 703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 70 time to evaluate : 0.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 31 TYR Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 105 TYR Chi-restraints excluded: chain H residue 192 VAL Chi-restraints excluded: chain H residue 202 TYR Chi-restraints excluded: chain H residue 215 VAL Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 50 SER Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain L residue 108 ILE Chi-restraints excluded: chain L residue 198 VAL Chi-restraints excluded: chain A residue 5 MET Chi-restraints excluded: chain A residue 93 HIS Chi-restraints excluded: chain A residue 214 THR Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain B residue 40 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 32 optimal weight: 0.7980 chunk 79 optimal weight: 1.9990 chunk 56 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 0 optimal weight: 7.9990 chunk 22 optimal weight: 2.9990 chunk 24 optimal weight: 0.4980 chunk 68 optimal weight: 5.9990 chunk 23 optimal weight: 0.6980 chunk 12 optimal weight: 20.0000 chunk 66 optimal weight: 1.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 242 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4530 r_free = 0.4530 target = 0.141017 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.106438 restraints weight = 13523.192| |-----------------------------------------------------------------------------| r_work (start): 0.3986 rms_B_bonded: 3.06 r_work: 0.3864 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3864 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7040 moved from start: 0.3830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 6580 Z= 0.186 Angle : 0.819 10.497 8949 Z= 0.424 Chirality : 0.048 0.232 967 Planarity : 0.006 0.075 1161 Dihedral : 7.385 57.699 896 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 20.79 Ramachandran Plot: Outliers : 0.25 % Allowed : 16.02 % Favored : 83.73 % Rotamer: Outliers : 2.99 % Allowed : 21.19 % Favored : 75.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.39 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.33 (0.28), residues: 805 helix: -0.25 (0.55), residues: 100 sheet: -1.43 (0.32), residues: 241 loop : -3.26 (0.27), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG L 24 TYR 0.026 0.003 TYR L 49 PHE 0.025 0.002 PHE B 90 TRP 0.022 0.002 TRP H 47 HIS 0.010 0.001 HIS B 51 Details of bonding type rmsd covalent geometry : bond 0.00428 ( 6573) covalent geometry : angle 0.81790 ( 8935) SS BOND : bond 0.00566 ( 7) SS BOND : angle 1.22867 ( 14) hydrogen bonds : bond 0.03757 ( 145) hydrogen bonds : angle 6.15238 ( 417) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1997.48 seconds wall clock time: 34 minutes 56.44 seconds (2096.44 seconds total)