Starting phenix.real_space_refine on Thu Jul 24 23:57:52 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8uzc_42839/07_2025/8uzc_42839.cif Found real_map, /net/cci-nas-00/data/ceres_data/8uzc_42839/07_2025/8uzc_42839.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8uzc_42839/07_2025/8uzc_42839.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8uzc_42839/07_2025/8uzc_42839.map" model { file = "/net/cci-nas-00/data/ceres_data/8uzc_42839/07_2025/8uzc_42839.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8uzc_42839/07_2025/8uzc_42839.cif" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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= -0.002 sd= 0.055 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 S 15 5.16 5 C 2182 2.51 5 N 610 2.21 5 O 657 1.98 5 H 3367 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 6831 Number of models: 1 Model: "" Number of chains: 3 Chain: "H" Number of atoms: 1834 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 1834 Classifications: {'peptide': 123} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 2, 'TRANS': 120} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'PHE:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "L" Number of atoms: 1613 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 1613 Classifications: {'peptide': 104} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 7, 'TRANS': 96} Chain breaks: 1 Chain: "A" Number of atoms: 3384 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 3384 Classifications: {'peptide': 216} Link IDs: {'PTRANS': 13, 'TRANS': 202} Chain breaks: 2 Time building chain proxies: 4.49, per 1000 atoms: 0.66 Number of scatterers: 6831 At special positions: 0 Unit cell: (68.739, 79.154, 89.569, 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 15 16.00 O 657 8.00 N 610 7.00 C 2182 6.00 H 3367 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " 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: 1.73 Conformation dependent library (CDL) restraints added in 650.1 milliseconds 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 808 Finding SS restraints... Secondary structure from input PDB file: 6 helices and 10 sheets defined 9.9% alpha, 25.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.63 Creating SS restraints... Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.721A pdb=" N TYR H 32 " --> pdb=" O PHE H 29 " (cutoff:3.500A) Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.535A pdb=" N PHE L 83 " --> pdb=" O PRO L 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 65 through 72 Processing helix chain 'A' and resid 73 through 80 removed outlier: 5.355A pdb=" N GLY A 78 " --> pdb=" O GLN A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 116 Processing helix chain 'A' and resid 156 through 160 removed outlier: 3.518A pdb=" N THR A 160 " --> pdb=" O LEU A 157 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'H' and resid 3 through 7 removed outlier: 3.618A pdb=" N VAL H 5 " --> pdb=" O ALA H 23 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ALA H 23 " --> pdb=" O VAL H 5 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N LEU H 20 " --> pdb=" O LEU H 80 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'H' and resid 10 through 12 removed outlier: 5.826A pdb=" N GLY H 10 " --> pdb=" O THR H 110 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'L' and resid 10 through 13 Processing sheet with id=AA4, first strand: chain 'L' and resid 19 through 22 Processing sheet with id=AA5, first strand: chain 'L' and resid 48 through 50 removed outlier: 6.528A pdb=" N ASN L 53 " --> pdb=" O TYR L 49 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 86 through 88 removed outlier: 5.641A pdb=" N PHE A 87 " --> pdb=" O MET A 268 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'A' and resid 120 through 122 removed outlier: 3.555A pdb=" N LYS A 121 " --> pdb=" O TYR A 257 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N TYR A 257 " --> pdb=" O LYS A 121 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N GLY A 256 " --> pdb=" O ILE A 179 " (cutoff:3.500A) removed outlier: 4.963A pdb=" N ILE A 179 " --> pdb=" O GLY A 256 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 120 through 122 removed outlier: 3.555A pdb=" N LYS A 121 " --> pdb=" O TYR A 257 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N TYR A 257 " --> pdb=" O LYS A 121 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N GLY A 256 " --> pdb=" O ILE A 179 " (cutoff:3.500A) removed outlier: 4.963A pdb=" N ILE A 179 " --> pdb=" O GLY A 256 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 136 through 141 removed outlier: 3.611A pdb=" N SER A 146 " --> pdb=" O SER A 136 " (cutoff:3.500A) removed outlier: 7.898A pdb=" N ALA A 138 " --> pdb=" O SER A 144 " (cutoff:3.500A) removed outlier: 8.733A pdb=" N SER A 144 " --> pdb=" O ALA A 138 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 167 through 169 83 hydrogen bonds defined for protein. 189 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: 2.33 Time building geometry restraints manager: 2.14 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 3361 1.03 - 1.23: 33 1.23 - 1.43: 1515 1.43 - 1.62: 1982 1.62 - 1.82: 20 Bond restraints: 6911 Sorted by residual: bond pdb=" CA PHE H 52A" pdb=" C PHE H 52A" ideal model delta sigma weight residual 1.523 1.465 0.058 1.34e-02 5.57e+03 1.86e+01 bond pdb=" CA ASP H 53 " pdb=" C ASP H 53 " ideal model delta sigma weight residual 1.524 1.465 0.059 1.40e-02 5.10e+03 1.79e+01 bond pdb=" CA SER H 55 " pdb=" C SER H 55 " ideal model delta sigma weight residual 1.523 1.472 0.051 1.28e-02 6.10e+03 1.61e+01 bond pdb=" N GLN H 1 " pdb=" H3 GLN H 1 " ideal model delta sigma weight residual 0.890 0.960 -0.070 2.00e-02 2.50e+03 1.24e+01 bond pdb=" N GLU L 1 " pdb=" H3 GLU L 1 " ideal model delta sigma weight residual 0.890 0.960 -0.070 2.00e-02 2.50e+03 1.24e+01 ... (remaining 6906 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.64: 12115 1.64 - 3.28: 246 3.28 - 4.92: 32 4.92 - 6.57: 2 6.57 - 8.21: 3 Bond angle restraints: 12398 Sorted by residual: angle pdb=" N SER H 55 " pdb=" CA SER H 55 " pdb=" C SER H 55 " ideal model delta sigma weight residual 112.94 107.37 5.57 1.41e+00 5.03e-01 1.56e+01 angle pdb=" O SER H 52 " pdb=" C SER H 52 " pdb=" N PHE H 52A" ideal model delta sigma weight residual 122.03 125.58 -3.55 1.08e+00 8.57e-01 1.08e+01 angle pdb=" N ARG A 220 " pdb=" CA ARG A 220 " pdb=" C ARG A 220 " ideal model delta sigma weight residual 108.07 110.92 -2.85 8.90e-01 1.26e+00 1.03e+01 angle pdb=" N TYR H 100A" pdb=" CA TYR H 100A" pdb=" C TYR H 100A" ideal model delta sigma weight residual 114.75 110.72 4.03 1.26e+00 6.30e-01 1.02e+01 angle pdb=" N GLY H 10 " pdb=" CA GLY H 10 " pdb=" C GLY H 10 " ideal model delta sigma weight residual 110.20 114.40 -4.20 1.32e+00 5.74e-01 1.01e+01 ... (remaining 12393 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 2861 17.94 - 35.89: 337 35.89 - 53.83: 70 53.83 - 71.78: 17 71.78 - 89.72: 7 Dihedral angle restraints: 3292 sinusoidal: 1777 harmonic: 1515 Sorted by residual: dihedral pdb=" CA TRP A 153 " pdb=" C TRP A 153 " pdb=" N LEU A 154 " pdb=" CA LEU A 154 " ideal model delta harmonic sigma weight residual -180.00 -159.93 -20.07 0 5.00e+00 4.00e-02 1.61e+01 dihedral pdb=" CB CYS H 22 " pdb=" SG CYS H 22 " pdb=" SG CYS H 92 " pdb=" CB CYS H 92 " ideal model delta sinusoidal sigma weight residual 93.00 60.69 32.31 1 1.00e+01 1.00e-02 1.49e+01 dihedral pdb=" CA CYS A 64 " pdb=" C CYS A 64 " pdb=" N THR A 65 " pdb=" CA THR A 65 " ideal model delta harmonic sigma weight residual 180.00 161.10 18.90 0 5.00e+00 4.00e-02 1.43e+01 ... (remaining 3289 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 302 0.030 - 0.061: 148 0.061 - 0.091: 29 0.091 - 0.122: 33 0.122 - 0.152: 6 Chirality restraints: 518 Sorted by residual: chirality pdb=" CA ILE L 48 " pdb=" N ILE L 48 " pdb=" C ILE L 48 " pdb=" CB ILE L 48 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.78e-01 chirality pdb=" CA ILE H 51 " pdb=" N ILE H 51 " pdb=" C ILE H 51 " pdb=" CB ILE H 51 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.20e-01 chirality pdb=" CA ILE A 214 " pdb=" N ILE A 214 " pdb=" C ILE A 214 " pdb=" CB ILE A 214 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.97e-01 ... (remaining 515 not shown) Planarity restraints: 1032 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER H 52 " 0.013 2.00e-02 2.50e+03 2.83e-02 7.99e+00 pdb=" C SER H 52 " -0.049 2.00e-02 2.50e+03 pdb=" O SER H 52 " 0.019 2.00e-02 2.50e+03 pdb=" N PHE H 52A" 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 229 " 0.241 9.50e-02 1.11e+02 8.05e-02 7.13e+00 pdb=" NE ARG A 229 " -0.014 2.00e-02 2.50e+03 pdb=" CZ ARG A 229 " -0.004 2.00e-02 2.50e+03 pdb=" NH1 ARG A 229 " 0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG A 229 " 0.007 2.00e-02 2.50e+03 pdb="HH11 ARG A 229 " -0.002 2.00e-02 2.50e+03 pdb="HH12 ARG A 229 " -0.000 2.00e-02 2.50e+03 pdb="HH21 ARG A 229 " 0.002 2.00e-02 2.50e+03 pdb="HH22 ARG A 229 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER H 55 " -0.014 2.00e-02 2.50e+03 2.56e-02 6.56e+00 pdb=" N LYS H 56 " 0.044 2.00e-02 2.50e+03 pdb=" CA LYS H 56 " -0.011 2.00e-02 2.50e+03 pdb=" H LYS H 56 " -0.020 2.00e-02 2.50e+03 ... (remaining 1029 not shown) Histogram of nonbonded interaction distances: 1.46 - 2.09: 151 2.09 - 2.72: 11512 2.72 - 3.34: 19075 3.34 - 3.97: 24056 3.97 - 4.60: 37864 Nonbonded interactions: 92658 Sorted by model distance: nonbonded pdb=" OE1 GLU L 81 " pdb=" H GLU L 81 " model vdw 1.462 2.450 nonbonded pdb=" OE1 GLN H 105 " pdb=" H GLN H 105 " model vdw 1.586 2.450 nonbonded pdb=" OD1 ASP H 61 " pdb="HH22 ARG H 64 " model vdw 1.608 2.450 nonbonded pdb="HE21 GLN H 39 " pdb=" O LYS H 43 " model vdw 1.609 2.450 nonbonded pdb=" H TYR H 100F" pdb=" OH TYR L 36 " model vdw 1.647 2.450 ... (remaining 92653 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.690 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: 0.110 Extract box with map and model: 0.240 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 19.950 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.030 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:3.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.010 Total: 24.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6890 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 : 0.004 0.059 3546 Z= 0.233 Angle : 0.713 7.085 4807 Z= 0.412 Chirality : 0.044 0.152 518 Planarity : 0.006 0.107 618 Dihedral : 16.347 89.722 1287 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 14.20 Ramachandran Plot: Outliers : 0.23 % Allowed : 9.74 % Favored : 90.02 % Rotamer: Outliers : 3.45 % Allowed : 20.95 % Favored : 75.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.81 (0.39), residues: 431 helix: 0.22 (1.15), residues: 21 sheet: -2.36 (0.43), residues: 122 loop : -1.86 (0.36), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 103 HIS 0.002 0.001 HIS A 184 PHE 0.011 0.001 PHE L 98 TYR 0.015 0.002 TYR L 92 ARG 0.003 0.000 ARG A 90 Details of bonding type rmsd hydrogen bonds : bond 0.30237 ( 81) hydrogen bonds : angle 10.67771 ( 189) SS BOND : bond 0.00210 ( 2) SS BOND : angle 0.60409 ( 4) covalent geometry : bond 0.00402 ( 3544) covalent geometry : angle 0.71271 ( 4803) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 55 is missing expected H atoms. Skipping. Residue LYS 56 is missing expected H atoms. Skipping. Evaluate side-chains 71 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 58 time to evaluate : 0.547 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 4 MET cc_start: 0.7179 (mmt) cc_final: 0.6412 (mmm) REVERT: L 85 VAL cc_start: 0.6119 (t) cc_final: 0.5911 (t) REVERT: A 58 ILE cc_start: 0.8002 (mm) cc_final: 0.7718 (pt) REVERT: A 154 LEU cc_start: 0.7755 (tp) cc_final: 0.7485 (mm) outliers start: 13 outliers final: 12 residues processed: 65 average time/residue: 0.3753 time to fit residues: 29.2591 Evaluate side-chains 68 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 56 time to evaluate : 0.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain H residue 34 ILE Chi-restraints excluded: chain H residue 100 ILE Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 92 TYR Chi-restraints excluded: chain L residue 94 TRP Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 98 TYR Chi-restraints excluded: chain A residue 149 SER Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 246 ASN Chi-restraints excluded: chain A residue 277 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 36 optimal weight: 0.3980 chunk 32 optimal weight: 2.9990 chunk 18 optimal weight: 3.9990 chunk 11 optimal weight: 2.9990 chunk 21 optimal weight: 0.8980 chunk 17 optimal weight: 2.9990 chunk 33 optimal weight: 0.0270 chunk 13 optimal weight: 6.9990 chunk 20 optimal weight: 0.6980 chunk 25 optimal weight: 2.9990 chunk 39 optimal weight: 0.6980 overall best weight: 0.5438 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4233 r_free = 0.4233 target = 0.166700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.151205 restraints weight = 15310.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.155405 restraints weight = 8468.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.4128 r_free = 0.4128 target = 0.158375 restraints weight = 5410.280| |-----------------------------------------------------------------------------| r_work (final): 0.4145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6810 moved from start: 0.0948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 3546 Z= 0.116 Angle : 0.599 5.215 4807 Z= 0.313 Chirality : 0.045 0.174 518 Planarity : 0.006 0.084 618 Dihedral : 7.855 59.638 509 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.23 % Allowed : 8.12 % Favored : 91.65 % Rotamer: Outliers : 3.18 % Allowed : 20.95 % Favored : 75.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.78 (0.38), residues: 431 helix: 0.99 (1.15), residues: 21 sheet: -2.28 (0.42), residues: 132 loop : -1.90 (0.36), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP H 103 HIS 0.002 0.001 HIS H 35 PHE 0.009 0.001 PHE H 67 TYR 0.013 0.001 TYR L 49 ARG 0.002 0.000 ARG A 141 Details of bonding type rmsd hydrogen bonds : bond 0.04143 ( 81) hydrogen bonds : angle 7.37614 ( 189) SS BOND : bond 0.00262 ( 2) SS BOND : angle 0.99252 ( 4) covalent geometry : bond 0.00263 ( 3544) covalent geometry : angle 0.59814 ( 4803) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 55 is missing expected H atoms. Skipping. Residue LYS 56 is missing expected H atoms. Skipping. Evaluate side-chains 68 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 56 time to evaluate : 0.526 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 62 SER cc_start: 0.8008 (OUTLIER) cc_final: 0.7727 (t) REVERT: L 4 MET cc_start: 0.7159 (mmt) cc_final: 0.6150 (mmm) REVERT: A 58 ILE cc_start: 0.8102 (mm) cc_final: 0.7778 (pt) outliers start: 12 outliers final: 8 residues processed: 65 average time/residue: 0.3270 time to fit residues: 26.1699 Evaluate side-chains 61 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 52 time to evaluate : 0.558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 34 ILE Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain H residue 95 GLU Chi-restraints excluded: chain H residue 100 ILE Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 52 SER Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 98 TYR Chi-restraints excluded: chain A residue 228 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 13 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 chunk 12 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 42 optimal weight: 5.9990 chunk 24 optimal weight: 0.7980 chunk 20 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 14 optimal weight: 0.9990 chunk 15 optimal weight: 0.5980 chunk 34 optimal weight: 0.9980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 38 GLN ** A 75 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 = 0.4211 r_free = 0.4211 target = 0.164794 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.149147 restraints weight = 15559.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.153324 restraints weight = 8559.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4100 r_free = 0.4100 target = 0.156205 restraints weight = 5508.293| |-----------------------------------------------------------------------------| r_work (final): 0.4104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6897 moved from start: 0.1353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 3546 Z= 0.154 Angle : 0.602 5.027 4807 Z= 0.317 Chirality : 0.045 0.172 518 Planarity : 0.006 0.076 618 Dihedral : 6.798 56.861 499 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 11.12 Ramachandran Plot: Outliers : 0.23 % Allowed : 10.21 % Favored : 89.56 % Rotamer: Outliers : 4.51 % Allowed : 20.69 % Favored : 74.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.92 (0.39), residues: 431 helix: 0.85 (1.18), residues: 21 sheet: -2.34 (0.42), residues: 134 loop : -2.01 (0.36), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP L 94 HIS 0.003 0.001 HIS A 184 PHE 0.013 0.001 PHE L 98 TYR 0.015 0.002 TYR A 233 ARG 0.004 0.000 ARG A 150 Details of bonding type rmsd hydrogen bonds : bond 0.03813 ( 81) hydrogen bonds : angle 6.88287 ( 189) SS BOND : bond 0.00248 ( 2) SS BOND : angle 0.89961 ( 4) covalent geometry : bond 0.00358 ( 3544) covalent geometry : angle 0.60184 ( 4803) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 55 is missing expected H atoms. Skipping. Residue LYS 56 is missing expected H atoms. Skipping. Evaluate side-chains 73 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 56 time to evaluate : 0.504 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 62 SER cc_start: 0.8087 (OUTLIER) cc_final: 0.7790 (t) REVERT: L 4 MET cc_start: 0.7213 (mmt) cc_final: 0.6409 (mmm) REVERT: A 58 ILE cc_start: 0.8151 (mm) cc_final: 0.7885 (pt) REVERT: A 244 LEU cc_start: 0.6953 (OUTLIER) cc_final: 0.6208 (tt) outliers start: 17 outliers final: 11 residues processed: 66 average time/residue: 0.3277 time to fit residues: 26.4058 Evaluate side-chains 65 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 52 time to evaluate : 0.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 34 ILE Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain H residue 95 GLU Chi-restraints excluded: chain H residue 100 ILE Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 92 TYR Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 98 TYR Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 178 TYR Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 277 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 36 optimal weight: 0.0020 chunk 7 optimal weight: 0.8980 chunk 37 optimal weight: 0.8980 chunk 1 optimal weight: 3.9990 chunk 4 optimal weight: 0.9990 chunk 14 optimal weight: 4.9990 chunk 0 optimal weight: 3.9990 chunk 9 optimal weight: 0.9980 chunk 23 optimal weight: 2.9990 chunk 15 optimal weight: 0.7980 chunk 11 optimal weight: 0.1980 overall best weight: 0.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4234 r_free = 0.4234 target = 0.166952 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.151336 restraints weight = 15601.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.4092 r_free = 0.4092 target = 0.155698 restraints weight = 8493.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4128 r_free = 0.4128 target = 0.158626 restraints weight = 5357.252| |-----------------------------------------------------------------------------| r_work (final): 0.4133 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6841 moved from start: 0.1641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 3546 Z= 0.105 Angle : 0.549 4.892 4807 Z= 0.287 Chirality : 0.045 0.169 518 Planarity : 0.005 0.058 618 Dihedral : 6.581 54.847 499 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.23 % Allowed : 8.58 % Favored : 91.18 % Rotamer: Outliers : 3.18 % Allowed : 22.02 % Favored : 74.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.75 (0.39), residues: 431 helix: 1.45 (1.18), residues: 21 sheet: -2.36 (0.41), residues: 138 loop : -1.83 (0.36), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP L 94 HIS 0.002 0.001 HIS H 35 PHE 0.007 0.001 PHE L 98 TYR 0.011 0.001 TYR L 92 ARG 0.002 0.000 ARG A 229 Details of bonding type rmsd hydrogen bonds : bond 0.02916 ( 81) hydrogen bonds : angle 6.36728 ( 189) SS BOND : bond 0.00309 ( 2) SS BOND : angle 0.79908 ( 4) covalent geometry : bond 0.00244 ( 3544) covalent geometry : angle 0.54862 ( 4803) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 55 is missing expected H atoms. Skipping. Residue LYS 56 is missing expected H atoms. Skipping. Evaluate side-chains 70 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 58 time to evaluate : 0.522 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 62 SER cc_start: 0.8122 (OUTLIER) cc_final: 0.7783 (t) REVERT: A 58 ILE cc_start: 0.8027 (mm) cc_final: 0.7700 (pt) REVERT: A 244 LEU cc_start: 0.6883 (OUTLIER) cc_final: 0.6203 (tt) outliers start: 12 outliers final: 9 residues processed: 65 average time/residue: 0.4056 time to fit residues: 32.1383 Evaluate side-chains 64 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 53 time to evaluate : 0.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 34 ILE Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain H residue 95 GLU Chi-restraints excluded: chain H residue 100 ILE Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 98 TYR Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 277 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 14 optimal weight: 4.9990 chunk 2 optimal weight: 2.9990 chunk 42 optimal weight: 4.9990 chunk 13 optimal weight: 1.9990 chunk 5 optimal weight: 3.9990 chunk 29 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 7 optimal weight: 0.5980 chunk 16 optimal weight: 2.9990 chunk 17 optimal weight: 0.9980 chunk 26 optimal weight: 1.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 38 GLN A 156 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4171 r_free = 0.4171 target = 0.161068 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.145169 restraints weight = 15772.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.149178 restraints weight = 9086.411| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.151930 restraints weight = 5987.771| |-----------------------------------------------------------------------------| r_work (final): 0.4041 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7012 moved from start: 0.2089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.031 3546 Z= 0.202 Angle : 0.633 5.203 4807 Z= 0.340 Chirality : 0.047 0.176 518 Planarity : 0.006 0.069 618 Dihedral : 6.945 53.385 499 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 14.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.85 % Favored : 85.15 % Rotamer: Outliers : 5.31 % Allowed : 20.42 % Favored : 74.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.25 (0.37), residues: 431 helix: 0.44 (1.15), residues: 21 sheet: -2.46 (0.41), residues: 134 loop : -2.29 (0.34), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 234 HIS 0.004 0.001 HIS A 184 PHE 0.018 0.002 PHE L 98 TYR 0.022 0.002 TYR A 233 ARG 0.006 0.001 ARG A 150 Details of bonding type rmsd hydrogen bonds : bond 0.03482 ( 81) hydrogen bonds : angle 6.57908 ( 189) SS BOND : bond 0.00327 ( 2) SS BOND : angle 1.01890 ( 4) covalent geometry : bond 0.00474 ( 3544) covalent geometry : angle 0.63290 ( 4803) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 55 is missing expected H atoms. Skipping. Residue LYS 56 is missing expected H atoms. Skipping. Evaluate side-chains 75 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 55 time to evaluate : 0.582 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 62 SER cc_start: 0.8249 (OUTLIER) cc_final: 0.7896 (t) REVERT: L 4 MET cc_start: 0.7110 (mmt) cc_final: 0.6421 (mmm) REVERT: A 244 LEU cc_start: 0.7021 (OUTLIER) cc_final: 0.6329 (tt) outliers start: 20 outliers final: 15 residues processed: 67 average time/residue: 0.3910 time to fit residues: 31.2451 Evaluate side-chains 67 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 50 time to evaluate : 0.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 34 ILE Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain H residue 100 ILE Chi-restraints excluded: chain L residue 12 SER Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 37 GLN Chi-restraints excluded: chain L residue 94 TRP Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 98 TYR Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 156 HIS Chi-restraints excluded: chain A residue 178 TYR Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 252 ILE Chi-restraints excluded: chain A residue 277 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 2 optimal weight: 2.9990 chunk 37 optimal weight: 0.0970 chunk 42 optimal weight: 3.9990 chunk 12 optimal weight: 0.4980 chunk 8 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 36 optimal weight: 0.6980 chunk 6 optimal weight: 0.5980 chunk 40 optimal weight: 0.7980 chunk 14 optimal weight: 3.9990 overall best weight: 0.5378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 38 GLN ** A 75 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 = 0.4213 r_free = 0.4213 target = 0.164959 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.149283 restraints weight = 15449.214| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.153393 restraints weight = 8649.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.156225 restraints weight = 5576.544| |-----------------------------------------------------------------------------| r_work (final): 0.4092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6906 moved from start: 0.2184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 3546 Z= 0.115 Angle : 0.571 4.854 4807 Z= 0.300 Chirality : 0.045 0.167 518 Planarity : 0.008 0.162 618 Dihedral : 6.729 54.448 499 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 11.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.74 % Favored : 90.26 % Rotamer: Outliers : 3.71 % Allowed : 22.02 % Favored : 74.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.91 (0.38), residues: 431 helix: 1.11 (1.18), residues: 21 sheet: -2.31 (0.42), residues: 137 loop : -2.03 (0.35), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP L 94 HIS 0.008 0.001 HIS A 156 PHE 0.007 0.001 PHE L 98 TYR 0.011 0.001 TYR H 91 ARG 0.004 0.000 ARG H 19 Details of bonding type rmsd hydrogen bonds : bond 0.02824 ( 81) hydrogen bonds : angle 6.20157 ( 189) SS BOND : bond 0.00320 ( 2) SS BOND : angle 0.81128 ( 4) covalent geometry : bond 0.00261 ( 3544) covalent geometry : angle 0.57068 ( 4803) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 55 is missing expected H atoms. Skipping. Residue LYS 56 is missing expected H atoms. Skipping. Evaluate side-chains 68 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 54 time to evaluate : 0.549 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 62 SER cc_start: 0.8136 (OUTLIER) cc_final: 0.7855 (t) REVERT: L 81 GLU cc_start: 0.6890 (mp0) cc_final: 0.6662 (mp0) REVERT: A 58 ILE cc_start: 0.8124 (mm) cc_final: 0.7870 (mm) REVERT: A 71 LEU cc_start: 0.7342 (mp) cc_final: 0.7138 (mp) REVERT: A 244 LEU cc_start: 0.6925 (OUTLIER) cc_final: 0.6296 (tt) outliers start: 14 outliers final: 12 residues processed: 64 average time/residue: 0.3730 time to fit residues: 29.2463 Evaluate side-chains 65 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 51 time to evaluate : 0.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 34 ILE Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain H residue 100 ILE Chi-restraints excluded: chain L residue 12 SER Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 37 GLN Chi-restraints excluded: chain L residue 94 TRP Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 98 TYR Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 156 HIS Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 277 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 32 optimal weight: 0.9980 chunk 41 optimal weight: 0.9990 chunk 38 optimal weight: 1.9990 chunk 42 optimal weight: 5.9990 chunk 40 optimal weight: 0.9990 chunk 24 optimal weight: 0.6980 chunk 29 optimal weight: 0.5980 chunk 7 optimal weight: 1.9990 chunk 8 optimal weight: 0.9980 chunk 34 optimal weight: 0.9990 chunk 15 optimal weight: 0.5980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 38 GLN ** A 75 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 = 0.4209 r_free = 0.4209 target = 0.165043 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.148412 restraints weight = 15372.304| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.152632 restraints weight = 8657.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.4087 r_free = 0.4087 target = 0.155507 restraints weight = 5651.608| |-----------------------------------------------------------------------------| r_work (final): 0.4072 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6904 moved from start: 0.2408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 3546 Z= 0.126 Angle : 0.565 4.928 4807 Z= 0.297 Chirality : 0.045 0.171 518 Planarity : 0.008 0.152 618 Dihedral : 6.560 53.459 499 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 12.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.37 % Favored : 88.63 % Rotamer: Outliers : 4.24 % Allowed : 22.28 % Favored : 73.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.99 (0.38), residues: 431 helix: 1.20 (1.17), residues: 21 sheet: -2.49 (0.41), residues: 131 loop : -2.04 (0.35), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP L 94 HIS 0.004 0.001 HIS A 156 PHE 0.009 0.001 PHE L 98 TYR 0.014 0.002 TYR L 92 ARG 0.007 0.001 ARG H 19 Details of bonding type rmsd hydrogen bonds : bond 0.02914 ( 81) hydrogen bonds : angle 6.10150 ( 189) SS BOND : bond 0.00280 ( 2) SS BOND : angle 0.82443 ( 4) covalent geometry : bond 0.00297 ( 3544) covalent geometry : angle 0.56445 ( 4803) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 55 is missing expected H atoms. Skipping. Residue LYS 56 is missing expected H atoms. Skipping. Evaluate side-chains 69 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 53 time to evaluate : 0.587 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 62 SER cc_start: 0.8193 (OUTLIER) cc_final: 0.7894 (t) REVERT: A 58 ILE cc_start: 0.8119 (mm) cc_final: 0.7881 (mm) REVERT: A 244 LEU cc_start: 0.6969 (OUTLIER) cc_final: 0.6313 (tt) outliers start: 16 outliers final: 11 residues processed: 63 average time/residue: 0.3132 time to fit residues: 24.8733 Evaluate side-chains 64 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 51 time to evaluate : 0.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain H residue 100 ILE Chi-restraints excluded: chain L residue 12 SER Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 37 GLN Chi-restraints excluded: chain L residue 94 TRP Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 98 TYR Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 156 HIS Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 277 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 12 optimal weight: 3.9990 chunk 19 optimal weight: 0.9980 chunk 29 optimal weight: 2.9990 chunk 5 optimal weight: 0.0670 chunk 22 optimal weight: 2.9990 chunk 32 optimal weight: 0.1980 chunk 9 optimal weight: 0.9990 chunk 16 optimal weight: 0.9980 chunk 14 optimal weight: 2.9990 chunk 31 optimal weight: 0.6980 chunk 36 optimal weight: 0.0020 overall best weight: 0.3926 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 38 GLN ** A 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 152 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4246 r_free = 0.4246 target = 0.168140 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.151307 restraints weight = 15450.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.155688 restraints weight = 8619.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4127 r_free = 0.4127 target = 0.158684 restraints weight = 5560.439| |-----------------------------------------------------------------------------| r_work (final): 0.4115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6863 moved from start: 0.2662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 3546 Z= 0.098 Angle : 0.544 5.957 4807 Z= 0.283 Chirality : 0.044 0.165 518 Planarity : 0.007 0.135 618 Dihedral : 6.102 53.521 497 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.82 % Favored : 91.18 % Rotamer: Outliers : 2.92 % Allowed : 22.81 % Favored : 74.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.89 (0.38), residues: 431 helix: 0.17 (1.05), residues: 27 sheet: -2.31 (0.43), residues: 131 loop : -1.99 (0.35), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP L 94 HIS 0.001 0.000 HIS H 35 PHE 0.006 0.001 PHE H 29 TYR 0.011 0.001 TYR H 32 ARG 0.005 0.000 ARG H 19 Details of bonding type rmsd hydrogen bonds : bond 0.02676 ( 81) hydrogen bonds : angle 5.86059 ( 189) SS BOND : bond 0.00296 ( 2) SS BOND : angle 0.69208 ( 4) covalent geometry : bond 0.00228 ( 3544) covalent geometry : angle 0.54382 ( 4803) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 55 is missing expected H atoms. Skipping. Residue LYS 56 is missing expected H atoms. Skipping. Evaluate side-chains 62 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 51 time to evaluate : 0.572 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 ILE cc_start: 0.8073 (mm) cc_final: 0.7826 (mm) REVERT: A 244 LEU cc_start: 0.6871 (OUTLIER) cc_final: 0.6327 (tt) outliers start: 11 outliers final: 9 residues processed: 58 average time/residue: 0.3064 time to fit residues: 22.1527 Evaluate side-chains 60 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 50 time to evaluate : 0.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 100 ILE Chi-restraints excluded: chain L residue 12 SER Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 37 GLN Chi-restraints excluded: chain L residue 94 TRP Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 98 TYR Chi-restraints excluded: chain A residue 156 HIS Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain A residue 244 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 15 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 20 optimal weight: 0.7980 chunk 22 optimal weight: 2.9990 chunk 35 optimal weight: 0.5980 chunk 29 optimal weight: 0.0980 chunk 30 optimal weight: 2.9990 chunk 24 optimal weight: 0.8980 chunk 37 optimal weight: 0.9980 chunk 19 optimal weight: 1.9990 chunk 41 optimal weight: 0.9980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 75 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 = 0.4234 r_free = 0.4234 target = 0.167012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.150493 restraints weight = 15413.065| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.154653 restraints weight = 8608.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4114 r_free = 0.4114 target = 0.157595 restraints weight = 5641.298| |-----------------------------------------------------------------------------| r_work (final): 0.4100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6901 moved from start: 0.2787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3546 Z= 0.116 Angle : 0.552 6.654 4807 Z= 0.289 Chirality : 0.044 0.169 518 Planarity : 0.007 0.135 618 Dihedral : 6.081 51.604 497 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 10.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.51 % Favored : 90.49 % Rotamer: Outliers : 3.45 % Allowed : 22.55 % Favored : 74.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.89 (0.38), residues: 431 helix: 0.19 (1.06), residues: 27 sheet: -2.28 (0.42), residues: 131 loop : -2.01 (0.35), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP L 94 HIS 0.001 0.001 HIS A 156 PHE 0.010 0.001 PHE L 98 TYR 0.013 0.001 TYR H 91 ARG 0.009 0.000 ARG H 19 Details of bonding type rmsd hydrogen bonds : bond 0.02708 ( 81) hydrogen bonds : angle 5.80650 ( 189) SS BOND : bond 0.00317 ( 2) SS BOND : angle 0.85875 ( 4) covalent geometry : bond 0.00276 ( 3544) covalent geometry : angle 0.55186 ( 4803) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 55 is missing expected H atoms. Skipping. Residue LYS 56 is missing expected H atoms. Skipping. Evaluate side-chains 63 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 50 time to evaluate : 0.559 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 ILE cc_start: 0.8122 (mm) cc_final: 0.7891 (mm) REVERT: A 244 LEU cc_start: 0.6948 (OUTLIER) cc_final: 0.6428 (tt) outliers start: 13 outliers final: 12 residues processed: 58 average time/residue: 0.3079 time to fit residues: 22.3400 Evaluate side-chains 63 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 50 time to evaluate : 0.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 91 TYR Chi-restraints excluded: chain H residue 100 ILE Chi-restraints excluded: chain L residue 12 SER Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 37 GLN Chi-restraints excluded: chain L residue 94 TRP Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 98 TYR Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 156 HIS Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain A residue 244 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 17 optimal weight: 1.9990 chunk 7 optimal weight: 0.5980 chunk 42 optimal weight: 4.9990 chunk 18 optimal weight: 0.9990 chunk 19 optimal weight: 0.6980 chunk 39 optimal weight: 1.9990 chunk 32 optimal weight: 0.3980 chunk 8 optimal weight: 0.4980 chunk 5 optimal weight: 0.9980 chunk 22 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 75 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 = 0.4200 r_free = 0.4200 target = 0.164527 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.147493 restraints weight = 15620.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.151952 restraints weight = 8375.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.155013 restraints weight = 5294.935| |-----------------------------------------------------------------------------| r_work (final): 0.4099 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6859 moved from start: 0.2827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 3546 Z= 0.116 Angle : 0.561 6.576 4807 Z= 0.294 Chirality : 0.044 0.169 518 Planarity : 0.007 0.133 618 Dihedral : 6.041 50.854 497 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 10.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.74 % Favored : 90.26 % Rotamer: Outliers : 3.71 % Allowed : 22.55 % Favored : 73.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.88 (0.38), residues: 431 helix: 0.24 (1.06), residues: 27 sheet: -2.19 (0.43), residues: 131 loop : -2.06 (0.35), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP L 94 HIS 0.001 0.001 HIS A 184 PHE 0.008 0.001 PHE L 98 TYR 0.016 0.001 TYR H 32 ARG 0.010 0.000 ARG H 19 Details of bonding type rmsd hydrogen bonds : bond 0.02664 ( 81) hydrogen bonds : angle 5.78313 ( 189) SS BOND : bond 0.00307 ( 2) SS BOND : angle 0.78835 ( 4) covalent geometry : bond 0.00278 ( 3544) covalent geometry : angle 0.56125 ( 4803) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 55 is missing expected H atoms. Skipping. Residue LYS 56 is missing expected H atoms. Skipping. Evaluate side-chains 63 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 49 time to evaluate : 0.741 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 81 GLU cc_start: 0.7209 (mp0) cc_final: 0.6810 (mp0) REVERT: A 58 ILE cc_start: 0.8144 (mm) cc_final: 0.7926 (mm) REVERT: A 244 LEU cc_start: 0.6957 (OUTLIER) cc_final: 0.6411 (tt) outliers start: 14 outliers final: 13 residues processed: 57 average time/residue: 0.3349 time to fit residues: 24.6888 Evaluate side-chains 63 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 49 time to evaluate : 0.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 91 TYR Chi-restraints excluded: chain H residue 100 ILE Chi-restraints excluded: chain L residue 12 SER Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 37 GLN Chi-restraints excluded: chain L residue 94 TRP Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 98 TYR Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 156 HIS Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 277 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 26 optimal weight: 0.4980 chunk 22 optimal weight: 2.9990 chunk 13 optimal weight: 3.9990 chunk 25 optimal weight: 0.9980 chunk 28 optimal weight: 0.9980 chunk 18 optimal weight: 0.4980 chunk 39 optimal weight: 0.6980 chunk 6 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 38 GLN ** A 75 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 = 0.4220 r_free = 0.4220 target = 0.165946 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.149540 restraints weight = 15553.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.153638 restraints weight = 8710.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4101 r_free = 0.4101 target = 0.156530 restraints weight = 5715.122| |-----------------------------------------------------------------------------| r_work (final): 0.4094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6913 moved from start: 0.2903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 3546 Z= 0.123 Angle : 0.562 6.306 4807 Z= 0.294 Chirality : 0.044 0.171 518 Planarity : 0.007 0.133 618 Dihedral : 6.081 51.110 497 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.51 % Favored : 90.49 % Rotamer: Outliers : 3.45 % Allowed : 23.08 % Favored : 73.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.92 (0.38), residues: 431 helix: 0.22 (1.07), residues: 27 sheet: -2.20 (0.42), residues: 131 loop : -2.10 (0.35), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP L 94 HIS 0.001 0.001 HIS A 184 PHE 0.009 0.001 PHE L 98 TYR 0.014 0.001 TYR H 32 ARG 0.011 0.000 ARG H 19 Details of bonding type rmsd hydrogen bonds : bond 0.02739 ( 81) hydrogen bonds : angle 5.76693 ( 189) SS BOND : bond 0.00308 ( 2) SS BOND : angle 0.88666 ( 4) covalent geometry : bond 0.00292 ( 3544) covalent geometry : angle 0.56143 ( 4803) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4083.19 seconds wall clock time: 71 minutes 46.19 seconds (4306.19 seconds total)