Starting phenix.real_space_refine on Fri Aug 22 14:04:02 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7yp1_33992/08_2025/7yp1_33992.cif Found real_map, /net/cci-nas-00/data/ceres_data/7yp1_33992/08_2025/7yp1_33992.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.54 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7yp1_33992/08_2025/7yp1_33992.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7yp1_33992/08_2025/7yp1_33992.map" model { file = "/net/cci-nas-00/data/ceres_data/7yp1_33992/08_2025/7yp1_33992.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7yp1_33992/08_2025/7yp1_33992.cif" } resolution = 3.54 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= 0.013 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 17 5.16 5 C 2411 2.51 5 N 620 2.21 5 O 722 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 3770 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 1482 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1482 Classifications: {'peptide': 185} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 9, 'TRANS': 173} Chain breaks: 3 Chain: "B" Number of atoms: 588 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 588 Classifications: {'peptide': 77} Link IDs: {'TRANS': 76} Chain breaks: 1 Chain: "D" Number of atoms: 865 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 865 Classifications: {'peptide': 115} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 109} Chain: "G" Number of atoms: 835 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 835 Classifications: {'peptide': 113} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 107} Time building chain proxies: 0.79, per 1000 atoms: 0.21 Number of scatterers: 3770 At special positions: 0 Unit cell: (83.246, 71.576, 87.136, 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 17 16.00 O 722 8.00 N 620 7.00 C 2411 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 93 " distance=2.03 Simple disulfide: pdb=" SG CYS G 23 " - pdb=" SG CYS G 88 " distance=2.04 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: 0.21 Conformation dependent library (CDL) restraints added in 142.6 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 948 Ramachandran restraints generated. 474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 894 Finding SS restraints... Secondary structure from input PDB file: 11 helices and 10 sheets defined 16.9% alpha, 22.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.08 Creating SS restraints... Processing helix chain 'A' and resid 42 through 47 removed outlier: 3.665A pdb=" N VAL A 47 " --> pdb=" O LEU A 43 " (cutoff:3.500A) Processing helix chain 'A' and resid 51 through 60 removed outlier: 3.690A pdb=" N TRP A 56 " --> pdb=" O PRO A 52 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N ARG A 57 " --> pdb=" O GLU A 53 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N GLU A 58 " --> pdb=" O ALA A 54 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ASN A 60 " --> pdb=" O TRP A 56 " (cutoff:3.500A) Processing helix chain 'A' and resid 67 through 73 removed outlier: 4.276A pdb=" N ARG A 71 " --> pdb=" O SER A 67 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LYS A 73 " --> pdb=" O LEU A 69 " (cutoff:3.500A) Processing helix chain 'A' and resid 124 through 131 removed outlier: 3.533A pdb=" N PHE A 131 " --> pdb=" O GLU A 127 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 215 Processing helix chain 'B' and resid 41 through 45 removed outlier: 3.928A pdb=" N ILE B 45 " --> pdb=" O LEU B 42 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 94 removed outlier: 3.995A pdb=" N SER B 87 " --> pdb=" O LEU B 83 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N PHE B 88 " --> pdb=" O ASN B 84 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N SER B 91 " --> pdb=" O SER B 87 " (cutoff:3.500A) Processing helix chain 'B' and resid 103 through 117 removed outlier: 3.667A pdb=" N LEU B 107 " --> pdb=" O HIS B 103 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLU B 112 " --> pdb=" O LEU B 108 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 123 Processing helix chain 'D' and resid 84 through 88 removed outlier: 3.913A pdb=" N THR D 88 " --> pdb=" O THR D 85 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 83 removed outlier: 3.694A pdb=" N ASP G 82 " --> pdb=" O GLU G 79 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N ALA G 83 " --> pdb=" O CYS G 80 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 79 through 83' Processing sheet with id=AA1, first strand: chain 'A' and resid 32 through 34 removed outlier: 3.722A pdb=" N ILE B 48 " --> pdb=" O LYS A 24 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ASP A 28 " --> pdb=" O LEU B 50 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ASP B 47 " --> pdb=" O ASN B 65 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 135 through 138 removed outlier: 3.588A pdb=" N GLY A 135 " --> pdb=" O CYS A 153 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N LEU A 151 " --> pdb=" O MET A 137 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 156 through 158 removed outlier: 3.568A pdb=" N MET A 173 " --> pdb=" O SER A 156 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 177 through 182 removed outlier: 3.692A pdb=" N SER A 195 " --> pdb=" O VAL A 229 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N TYR A 224 " --> pdb=" O GLN A 220 " (cutoff:3.500A) removed outlier: 4.668A pdb=" N GLN A 220 " --> pdb=" O TYR A 224 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N LEU A 226 " --> pdb=" O SER A 218 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 61 through 62 removed outlier: 4.087A pdb=" N ALA B 62 " --> pdb=" O ALA B 80 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 4 through 7 Processing sheet with id=AA7, first strand: chain 'D' and resid 57 through 59 removed outlier: 6.819A pdb=" N TRP D 36 " --> pdb=" O ILE D 48 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N VAL D 50 " --> pdb=" O MET D 34 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N MET D 34 " --> pdb=" O VAL D 50 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'G' and resid 4 through 7 removed outlier: 3.657A pdb=" N THR G 5 " --> pdb=" O GLN G 24 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N GLN G 24 " --> pdb=" O THR G 5 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'G' and resid 10 through 13 removed outlier: 3.538A pdb=" N VAL G 109 " --> pdb=" O VAL G 11 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'G' and resid 53 through 54 removed outlier: 6.616A pdb=" N TRP G 35 " --> pdb=" O LEU G 47 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N TYR G 87 " --> pdb=" O TYR G 36 " (cutoff:3.500A) 99 hydrogen bonds defined for protein. 240 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: 0.37 Time building geometry restraints manager: 0.32 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 600 1.31 - 1.44: 1103 1.44 - 1.56: 2124 1.56 - 1.68: 2 1.68 - 1.81: 25 Bond restraints: 3854 Sorted by residual: bond pdb=" CA LEU G 73 " pdb=" C LEU G 73 " ideal model delta sigma weight residual 1.521 1.439 0.082 1.24e-02 6.50e+03 4.33e+01 bond pdb=" CA LYS G 63 " pdb=" C LYS G 63 " ideal model delta sigma weight residual 1.522 1.455 0.067 1.24e-02 6.50e+03 2.92e+01 bond pdb=" CA ILE G 75 " pdb=" CB ILE G 75 " ideal model delta sigma weight residual 1.538 1.490 0.048 9.80e-03 1.04e+04 2.43e+01 bond pdb=" C LEU G 73 " pdb=" O LEU G 73 " ideal model delta sigma weight residual 1.235 1.189 0.046 1.22e-02 6.72e+03 1.41e+01 bond pdb=" CA ILE G 75 " pdb=" C ILE G 75 " ideal model delta sigma weight residual 1.527 1.470 0.057 1.52e-02 4.33e+03 1.38e+01 ... (remaining 3849 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.70: 4820 1.70 - 3.41: 314 3.41 - 5.11: 78 5.11 - 6.82: 12 6.82 - 8.52: 11 Bond angle restraints: 5235 Sorted by residual: angle pdb=" N GLY G 66 " pdb=" CA GLY G 66 " pdb=" C GLY G 66 " ideal model delta sigma weight residual 111.95 116.83 -4.88 9.50e-01 1.11e+00 2.64e+01 angle pdb=" CA THR G 72 " pdb=" C THR G 72 " pdb=" N LEU G 73 " ideal model delta sigma weight residual 115.61 122.80 -7.19 1.45e+00 4.76e-01 2.46e+01 angle pdb=" N LEU G 73 " pdb=" CA LEU G 73 " pdb=" C LEU G 73 " ideal model delta sigma weight residual 109.24 102.14 7.10 1.67e+00 3.59e-01 1.81e+01 angle pdb=" N THR G 69 " pdb=" CA THR G 69 " pdb=" C THR G 69 " ideal model delta sigma weight residual 113.17 118.02 -4.85 1.26e+00 6.30e-01 1.48e+01 angle pdb=" N TYR A 213 " pdb=" CA TYR A 213 " pdb=" C TYR A 213 " ideal model delta sigma weight residual 109.81 118.22 -8.41 2.21e+00 2.05e-01 1.45e+01 ... (remaining 5230 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.44: 2015 17.44 - 34.88: 198 34.88 - 52.32: 33 52.32 - 69.77: 3 69.77 - 87.21: 4 Dihedral angle restraints: 2253 sinusoidal: 850 harmonic: 1403 Sorted by residual: dihedral pdb=" CB CYS G 23 " pdb=" SG CYS G 23 " pdb=" SG CYS G 88 " pdb=" CB CYS G 88 " ideal model delta sinusoidal sigma weight residual 93.00 157.67 -64.67 1 1.00e+01 1.00e-02 5.49e+01 dihedral pdb=" CA TYR A 235 " pdb=" C TYR A 235 " pdb=" N ALA A 236 " pdb=" CA ALA A 236 " ideal model delta harmonic sigma weight residual 180.00 151.20 28.80 0 5.00e+00 4.00e-02 3.32e+01 dihedral pdb=" CA ASP A 248 " pdb=" C ASP A 248 " pdb=" N MET A 249 " pdb=" CA MET A 249 " ideal model delta harmonic sigma weight residual 180.00 155.26 24.74 0 5.00e+00 4.00e-02 2.45e+01 ... (remaining 2250 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 414 0.057 - 0.114: 150 0.114 - 0.171: 30 0.171 - 0.228: 7 0.228 - 0.285: 3 Chirality restraints: 604 Sorted by residual: chirality pdb=" CA ARG G 61 " pdb=" N ARG G 61 " pdb=" C ARG G 61 " pdb=" CB ARG G 61 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 2.03e+00 chirality pdb=" CA THR G 69 " pdb=" N THR G 69 " pdb=" C THR G 69 " pdb=" CB THR G 69 " both_signs ideal model delta sigma weight residual False 2.53 2.25 0.27 2.00e-01 2.50e+01 1.86e+00 chirality pdb=" CB THR A 181 " pdb=" CA THR A 181 " pdb=" OG1 THR A 181 " pdb=" CG2 THR A 181 " both_signs ideal model delta sigma weight residual False 2.55 2.28 0.27 2.00e-01 2.50e+01 1.84e+00 ... (remaining 601 not shown) Planarity restraints: 652 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA A 124 " -0.048 5.00e-02 4.00e+02 7.23e-02 8.36e+00 pdb=" N PRO A 125 " 0.125 5.00e-02 4.00e+02 pdb=" CA PRO A 125 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO A 125 " -0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ARG D 102 " -0.012 2.00e-02 2.50e+03 2.48e-02 6.14e+00 pdb=" C ARG D 102 " 0.043 2.00e-02 2.50e+03 pdb=" O ARG D 102 " -0.016 2.00e-02 2.50e+03 pdb=" N PHE D 103 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS G 39 " -0.037 5.00e-02 4.00e+02 5.62e-02 5.06e+00 pdb=" N PRO G 40 " 0.097 5.00e-02 4.00e+02 pdb=" CA PRO G 40 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO G 40 " -0.031 5.00e-02 4.00e+02 ... (remaining 649 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 1106 2.80 - 3.33: 2870 3.33 - 3.85: 5796 3.85 - 4.38: 6517 4.38 - 4.90: 12039 Nonbonded interactions: 28328 Sorted by model distance: nonbonded pdb=" O SER A 251 " pdb=" OG SER A 251 " model vdw 2.275 3.040 nonbonded pdb=" O SER B 87 " pdb=" OG SER B 87 " model vdw 2.289 3.040 nonbonded pdb=" OG1 THR A 201 " pdb=" O ASP A 223 " model vdw 2.302 3.040 nonbonded pdb=" O PHE A 211 " pdb=" OH TYR B 115 " model vdw 2.314 3.040 nonbonded pdb=" O SER B 96 " pdb=" OG SER B 96 " model vdw 2.339 3.040 ... (remaining 28323 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=0.50 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: 7.360 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: 0.050 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 4.190 Find NCS groups from input model: 0.010 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:1.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 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 : 0.010 0.082 3856 Z= 0.517 Angle : 1.055 8.520 5239 Z= 0.592 Chirality : 0.065 0.285 604 Planarity : 0.007 0.072 652 Dihedral : 14.046 87.208 1353 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.92 % Favored : 90.08 % Rotamer: Outliers : 0.24 % Allowed : 11.81 % Favored : 87.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.22 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -5.19 (0.30), residues: 474 helix: -5.07 (0.16), residues: 84 sheet: -2.38 (0.40), residues: 151 loop : -3.56 (0.31), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 95 TYR 0.017 0.002 TYR A 132 PHE 0.021 0.003 PHE A 177 TRP 0.016 0.003 TRP D 33 HIS 0.008 0.002 HIS A 192 Details of bonding type rmsd covalent geometry : bond 0.01047 ( 3854) covalent geometry : angle 1.05487 ( 5235) SS BOND : bond 0.00830 ( 2) SS BOND : angle 1.50343 ( 4) hydrogen bonds : bond 0.28118 ( 99) hydrogen bonds : angle 10.29860 ( 240) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 948 Ramachandran restraints generated. 474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 948 Ramachandran restraints generated. 474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 73 time to evaluate : 0.141 Fit side-chains REVERT: B 78 ARG cc_start: 0.7685 (mmt180) cc_final: 0.6756 (mmm160) outliers start: 1 outliers final: 0 residues processed: 74 average time/residue: 0.0910 time to fit residues: 7.9326 Evaluate side-chains 65 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 65 time to evaluate : 0.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 24 optimal weight: 0.1980 chunk 26 optimal weight: 0.1980 chunk 2 optimal weight: 0.9990 chunk 16 optimal weight: 0.0870 chunk 32 optimal weight: 0.9980 chunk 31 optimal weight: 0.5980 chunk 25 optimal weight: 0.6980 chunk 19 optimal weight: 3.9990 chunk 30 optimal weight: 0.7980 chunk 22 optimal weight: 0.2980 chunk 37 optimal weight: 0.3980 overall best weight: 0.2358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 HIS ** A 234 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 = 0.3650 r_free = 0.3650 target = 0.148110 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.122297 restraints weight = 5248.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.126197 restraints weight = 3031.454| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.128808 restraints weight = 2133.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.130514 restraints weight = 1673.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.131461 restraints weight = 1414.474| |-----------------------------------------------------------------------------| r_work (final): 0.3437 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3494 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3494 r_free = 0.3494 target_work(ls_wunit_k1) = 0.133 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3477 r_free = 0.3477 target_work(ls_wunit_k1) = 0.132 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3477 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 moved from start: 0.1561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 3856 Z= 0.108 Angle : 0.569 6.782 5239 Z= 0.301 Chirality : 0.044 0.157 604 Planarity : 0.005 0.039 652 Dihedral : 5.663 42.665 530 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 1.45 % Allowed : 16.14 % Favored : 82.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.22 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.16 (0.34), residues: 474 helix: -4.14 (0.31), residues: 88 sheet: -1.67 (0.44), residues: 154 loop : -2.94 (0.34), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 102 TYR 0.009 0.001 TYR A 72 PHE 0.007 0.001 PHE D 105 TRP 0.008 0.001 TRP D 33 HIS 0.003 0.001 HIS A 26 Details of bonding type rmsd covalent geometry : bond 0.00247 ( 3854) covalent geometry : angle 0.56796 ( 5235) SS BOND : bond 0.00694 ( 2) SS BOND : angle 1.25836 ( 4) hydrogen bonds : bond 0.03787 ( 99) hydrogen bonds : angle 6.32564 ( 240) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 948 Ramachandran restraints generated. 474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 948 Ramachandran restraints generated. 474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 70 time to evaluate : 0.147 Fit side-chains REVERT: A 247 LYS cc_start: 0.8092 (mptt) cc_final: 0.7830 (mptt) REVERT: A 248 ASP cc_start: 0.8113 (m-30) cc_final: 0.7664 (t70) REVERT: B 78 ARG cc_start: 0.7706 (mmt180) cc_final: 0.6720 (mmm160) outliers start: 6 outliers final: 4 residues processed: 75 average time/residue: 0.0842 time to fit residues: 7.5213 Evaluate side-chains 67 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 63 time to evaluate : 0.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 CYS Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain D residue 64 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 16 optimal weight: 0.9980 chunk 26 optimal weight: 0.5980 chunk 37 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 35 optimal weight: 0.9980 chunk 8 optimal weight: 0.1980 chunk 45 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 41 optimal weight: 0.0570 chunk 34 optimal weight: 0.9980 overall best weight: 0.5698 ------------------------------------------------------------------------------- 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 = 0.3665 r_free = 0.3665 target = 0.149165 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.124520 restraints weight = 5171.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.127963 restraints weight = 3199.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.130202 restraints weight = 2341.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.131705 restraints weight = 1889.700| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.132867 restraints weight = 1624.005| |-----------------------------------------------------------------------------| r_work (final): 0.3450 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3450 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3450 r_free = 0.3450 target_work(ls_wunit_k1) = 0.130 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3449 r_free = 0.3449 target_work(ls_wunit_k1) = 0.130 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3449 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.1799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 3856 Z= 0.159 Angle : 0.565 6.579 5239 Z= 0.293 Chirality : 0.044 0.152 604 Planarity : 0.004 0.030 652 Dihedral : 5.375 38.571 530 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.54 % Favored : 93.46 % Rotamer: Outliers : 2.41 % Allowed : 19.28 % Favored : 78.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.22 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.71 (0.36), residues: 474 helix: -3.50 (0.40), residues: 90 sheet: -1.42 (0.44), residues: 156 loop : -2.74 (0.36), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 152 TYR 0.011 0.001 TYR D 47 PHE 0.009 0.001 PHE A 177 TRP 0.010 0.001 TRP D 33 HIS 0.003 0.001 HIS A 26 Details of bonding type rmsd covalent geometry : bond 0.00383 ( 3854) covalent geometry : angle 0.56422 ( 5235) SS BOND : bond 0.00699 ( 2) SS BOND : angle 1.06440 ( 4) hydrogen bonds : bond 0.03373 ( 99) hydrogen bonds : angle 5.64249 ( 240) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 948 Ramachandran restraints generated. 474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 948 Ramachandran restraints generated. 474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 68 time to evaluate : 0.138 Fit side-chains REVERT: A 248 ASP cc_start: 0.8076 (m-30) cc_final: 0.7640 (t70) REVERT: B 78 ARG cc_start: 0.7758 (mmt180) cc_final: 0.6903 (mmm160) outliers start: 10 outliers final: 7 residues processed: 77 average time/residue: 0.0848 time to fit residues: 7.8658 Evaluate side-chains 68 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 61 time to evaluate : 0.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 CYS Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain D residue 64 LYS Chi-restraints excluded: chain D residue 80 ILE Chi-restraints excluded: chain D residue 113 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 27 optimal weight: 0.0470 chunk 37 optimal weight: 0.8980 chunk 35 optimal weight: 0.0970 chunk 15 optimal weight: 0.9980 chunk 6 optimal weight: 0.9980 chunk 5 optimal weight: 0.9990 chunk 21 optimal weight: 0.8980 chunk 26 optimal weight: 0.7980 chunk 34 optimal weight: 0.5980 chunk 19 optimal weight: 4.9990 chunk 41 optimal weight: 0.0970 overall best weight: 0.3274 ------------------------------------------------------------------------------- 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 = 0.3494 r_free = 0.3494 target = 0.137330 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.112389 restraints weight = 5138.939| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.115641 restraints weight = 3258.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.117954 restraints weight = 2406.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.119402 restraints weight = 1944.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.120519 restraints weight = 1673.626| |-----------------------------------------------------------------------------| r_work (final): 0.3322 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3371 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3371 r_free = 0.3371 target_work(ls_wunit_k1) = 0.125 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3371 r_free = 0.3371 target_work(ls_wunit_k1) = 0.125 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3371 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.2114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 3856 Z= 0.104 Angle : 0.510 5.917 5239 Z= 0.264 Chirality : 0.042 0.143 604 Planarity : 0.004 0.033 652 Dihedral : 4.919 32.350 530 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 3.61 % Allowed : 19.28 % Favored : 77.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.22 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.17 (0.37), residues: 474 helix: -3.11 (0.45), residues: 91 sheet: -1.10 (0.43), residues: 156 loop : -2.36 (0.38), residues: 227 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 38 TYR 0.014 0.001 TYR A 213 PHE 0.007 0.001 PHE A 177 TRP 0.008 0.001 TRP D 33 HIS 0.002 0.001 HIS A 26 Details of bonding type rmsd covalent geometry : bond 0.00248 ( 3854) covalent geometry : angle 0.50923 ( 5235) SS BOND : bond 0.00587 ( 2) SS BOND : angle 1.06196 ( 4) hydrogen bonds : bond 0.02760 ( 99) hydrogen bonds : angle 5.19520 ( 240) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 948 Ramachandran restraints generated. 474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 948 Ramachandran restraints generated. 474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 64 time to evaluate : 0.145 Fit side-chains REVERT: A 179 MET cc_start: 0.8338 (OUTLIER) cc_final: 0.7659 (ttt) REVERT: A 248 ASP cc_start: 0.7998 (m-30) cc_final: 0.7526 (t70) REVERT: B 78 ARG cc_start: 0.7684 (mmt180) cc_final: 0.6650 (mmm160) REVERT: D 29 LEU cc_start: 0.8743 (OUTLIER) cc_final: 0.8414 (pp) outliers start: 15 outliers final: 9 residues processed: 74 average time/residue: 0.0744 time to fit residues: 6.7094 Evaluate side-chains 72 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 61 time to evaluate : 0.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 CYS Chi-restraints excluded: chain A residue 179 MET Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain B residue 117 SER Chi-restraints excluded: chain D residue 2 GLN Chi-restraints excluded: chain D residue 6 GLU Chi-restraints excluded: chain D residue 29 LEU Chi-restraints excluded: chain D residue 64 LYS Chi-restraints excluded: chain D residue 113 THR Chi-restraints excluded: chain G residue 101 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 41 optimal weight: 0.1980 chunk 45 optimal weight: 1.9990 chunk 17 optimal weight: 0.9990 chunk 15 optimal weight: 1.9990 chunk 44 optimal weight: 0.3980 chunk 34 optimal weight: 0.7980 chunk 0 optimal weight: 2.9990 chunk 18 optimal weight: 0.7980 chunk 13 optimal weight: 1.9990 chunk 22 optimal weight: 0.3980 chunk 12 optimal weight: 0.5980 overall best weight: 0.4780 ------------------------------------------------------------------------------- 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 = 0.3476 r_free = 0.3476 target = 0.135866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.110838 restraints weight = 5173.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.114029 restraints weight = 3279.975| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.116269 restraints weight = 2429.080| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.117704 restraints weight = 1975.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.118865 restraints weight = 1704.372| |-----------------------------------------------------------------------------| r_work (final): 0.3342 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3297 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3297 r_free = 0.3297 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3296 r_free = 0.3296 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3296 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8011 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 0.024 3856 Z= 0.135 Angle : 0.530 7.397 5239 Z= 0.272 Chirality : 0.043 0.154 604 Planarity : 0.003 0.029 652 Dihedral : 4.933 33.943 530 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.49 % Favored : 94.51 % Rotamer: Outliers : 3.86 % Allowed : 20.00 % Favored : 76.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.22 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.85 (0.38), residues: 474 helix: -2.84 (0.48), residues: 90 sheet: -0.81 (0.44), residues: 156 loop : -2.24 (0.39), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 152 TYR 0.010 0.001 TYR D 47 PHE 0.008 0.001 PHE A 177 TRP 0.009 0.001 TRP D 33 HIS 0.003 0.001 HIS A 26 Details of bonding type rmsd covalent geometry : bond 0.00322 ( 3854) covalent geometry : angle 0.52990 ( 5235) SS BOND : bond 0.00806 ( 2) SS BOND : angle 1.03270 ( 4) hydrogen bonds : bond 0.02881 ( 99) hydrogen bonds : angle 5.06316 ( 240) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 948 Ramachandran restraints generated. 474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 948 Ramachandran restraints generated. 474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 64 time to evaluate : 0.176 Fit side-chains REVERT: A 179 MET cc_start: 0.8338 (OUTLIER) cc_final: 0.7591 (ttt) REVERT: A 248 ASP cc_start: 0.8049 (m-30) cc_final: 0.7596 (t70) REVERT: B 78 ARG cc_start: 0.7686 (mmt180) cc_final: 0.6678 (mmm160) REVERT: D 10 ARG cc_start: 0.7398 (mtt180) cc_final: 0.7151 (ptm-80) REVERT: D 29 LEU cc_start: 0.8774 (OUTLIER) cc_final: 0.8475 (pp) outliers start: 16 outliers final: 9 residues processed: 75 average time/residue: 0.0785 time to fit residues: 7.1471 Evaluate side-chains 73 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 62 time to evaluate : 0.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 CYS Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 179 MET Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain B residue 117 SER Chi-restraints excluded: chain D residue 2 GLN Chi-restraints excluded: chain D residue 6 GLU Chi-restraints excluded: chain D residue 29 LEU Chi-restraints excluded: chain D residue 64 LYS Chi-restraints excluded: chain D residue 113 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 26 optimal weight: 0.3980 chunk 29 optimal weight: 0.9990 chunk 1 optimal weight: 0.3980 chunk 8 optimal weight: 0.5980 chunk 0 optimal weight: 0.8980 chunk 11 optimal weight: 0.9990 chunk 34 optimal weight: 0.9990 chunk 7 optimal weight: 0.6980 chunk 42 optimal weight: 3.9990 chunk 32 optimal weight: 0.8980 chunk 41 optimal weight: 0.6980 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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 = 0.3585 r_free = 0.3585 target = 0.142993 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.116754 restraints weight = 5262.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.120513 restraints weight = 3081.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.122949 restraints weight = 2200.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.124705 restraints weight = 1753.299| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.125836 restraints weight = 1492.319| |-----------------------------------------------------------------------------| r_work (final): 0.3424 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3366 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3366 r_free = 0.3366 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3366 r_free = 0.3366 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3366 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 moved from start: 0.2239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 3856 Z= 0.152 Angle : 0.541 6.938 5239 Z= 0.279 Chirality : 0.043 0.148 604 Planarity : 0.003 0.030 652 Dihedral : 4.965 35.016 530 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer: Outliers : 3.86 % Allowed : 20.24 % Favored : 75.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.22 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.72 (0.38), residues: 474 helix: -2.73 (0.49), residues: 90 sheet: -0.71 (0.44), residues: 156 loop : -2.17 (0.39), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 10 TYR 0.009 0.001 TYR G 49 PHE 0.008 0.001 PHE B 89 TRP 0.009 0.001 TRP D 33 HIS 0.003 0.001 HIS A 192 Details of bonding type rmsd covalent geometry : bond 0.00363 ( 3854) covalent geometry : angle 0.53980 ( 5235) SS BOND : bond 0.00856 ( 2) SS BOND : angle 1.14132 ( 4) hydrogen bonds : bond 0.02896 ( 99) hydrogen bonds : angle 5.00656 ( 240) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 948 Ramachandran restraints generated. 474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 948 Ramachandran restraints generated. 474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 61 time to evaluate : 0.146 Fit side-chains REVERT: A 179 MET cc_start: 0.8266 (OUTLIER) cc_final: 0.7595 (ttt) REVERT: A 184 ARG cc_start: 0.6875 (ttp80) cc_final: 0.6636 (mmt180) REVERT: A 248 ASP cc_start: 0.8051 (m-30) cc_final: 0.7601 (t70) REVERT: B 78 ARG cc_start: 0.7721 (mmt180) cc_final: 0.6763 (mmm160) REVERT: D 10 ARG cc_start: 0.7371 (mtt180) cc_final: 0.7145 (ptm-80) REVERT: D 29 LEU cc_start: 0.8803 (OUTLIER) cc_final: 0.8492 (pp) outliers start: 16 outliers final: 10 residues processed: 73 average time/residue: 0.0810 time to fit residues: 7.1008 Evaluate side-chains 72 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 60 time to evaluate : 0.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 CYS Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 179 MET Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain B residue 117 SER Chi-restraints excluded: chain D residue 2 GLN Chi-restraints excluded: chain D residue 4 VAL Chi-restraints excluded: chain D residue 29 LEU Chi-restraints excluded: chain D residue 64 LYS Chi-restraints excluded: chain D residue 113 THR Chi-restraints excluded: chain G residue 101 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 8 optimal weight: 0.1980 chunk 46 optimal weight: 0.6980 chunk 5 optimal weight: 0.9990 chunk 39 optimal weight: 0.9980 chunk 3 optimal weight: 1.9990 chunk 36 optimal weight: 0.5980 chunk 30 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 chunk 34 optimal weight: 0.8980 chunk 6 optimal weight: 1.9990 chunk 26 optimal weight: 0.5980 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 = 0.3554 r_free = 0.3554 target = 0.140828 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.114338 restraints weight = 5313.146| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.118175 restraints weight = 3080.241| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.120751 restraints weight = 2183.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.122455 restraints weight = 1731.973| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.123511 restraints weight = 1472.580| |-----------------------------------------------------------------------------| r_work (final): 0.3410 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3353 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3353 r_free = 0.3353 target_work(ls_wunit_k1) = 0.123 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3353 r_free = 0.3353 target_work(ls_wunit_k1) = 0.123 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3353 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8081 moved from start: 0.2274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 3856 Z= 0.159 Angle : 0.541 7.002 5239 Z= 0.280 Chirality : 0.043 0.147 604 Planarity : 0.003 0.031 652 Dihedral : 5.032 35.485 530 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer: Outliers : 3.86 % Allowed : 20.96 % Favored : 75.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.22 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.71 (0.37), residues: 474 helix: -2.68 (0.48), residues: 91 sheet: -0.70 (0.44), residues: 150 loop : -2.15 (0.39), residues: 233 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 152 TYR 0.009 0.001 TYR G 49 PHE 0.009 0.001 PHE B 89 TRP 0.010 0.001 TRP D 33 HIS 0.003 0.001 HIS A 26 Details of bonding type rmsd covalent geometry : bond 0.00381 ( 3854) covalent geometry : angle 0.54006 ( 5235) SS BOND : bond 0.00801 ( 2) SS BOND : angle 1.11720 ( 4) hydrogen bonds : bond 0.02889 ( 99) hydrogen bonds : angle 4.98397 ( 240) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 948 Ramachandran restraints generated. 474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 948 Ramachandran restraints generated. 474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 65 time to evaluate : 0.150 Fit side-chains REVERT: A 179 MET cc_start: 0.8265 (OUTLIER) cc_final: 0.7552 (ttt) REVERT: A 232 PHE cc_start: 0.7809 (OUTLIER) cc_final: 0.7436 (t80) REVERT: A 248 ASP cc_start: 0.8098 (m-30) cc_final: 0.7622 (t70) REVERT: B 78 ARG cc_start: 0.7743 (mmt180) cc_final: 0.6794 (mmm160) REVERT: D 10 ARG cc_start: 0.7346 (mtt180) cc_final: 0.7127 (ptm-80) REVERT: D 29 LEU cc_start: 0.8802 (OUTLIER) cc_final: 0.8510 (pp) outliers start: 16 outliers final: 11 residues processed: 76 average time/residue: 0.0819 time to fit residues: 7.4154 Evaluate side-chains 79 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 65 time to evaluate : 0.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 CYS Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 179 MET Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 232 PHE Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain B residue 117 SER Chi-restraints excluded: chain D residue 2 GLN Chi-restraints excluded: chain D residue 4 VAL Chi-restraints excluded: chain D residue 6 GLU Chi-restraints excluded: chain D residue 29 LEU Chi-restraints excluded: chain D residue 64 LYS Chi-restraints excluded: chain D residue 113 THR Chi-restraints excluded: chain G residue 101 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 13 optimal weight: 0.8980 chunk 5 optimal weight: 0.9990 chunk 15 optimal weight: 0.5980 chunk 9 optimal weight: 0.6980 chunk 27 optimal weight: 0.9990 chunk 45 optimal weight: 1.9990 chunk 8 optimal weight: 0.2980 chunk 3 optimal weight: 2.9990 chunk 43 optimal weight: 0.7980 chunk 29 optimal weight: 0.9980 chunk 33 optimal weight: 0.9980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 = 0.3526 r_free = 0.3526 target = 0.138447 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.111985 restraints weight = 5277.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.115710 restraints weight = 3041.150| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.118267 restraints weight = 2156.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.119859 restraints weight = 1704.736| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.121023 restraints weight = 1454.239| |-----------------------------------------------------------------------------| r_work (final): 0.3422 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3423 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3423 r_free = 0.3423 target_work(ls_wunit_k1) = 0.128 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3423 r_free = 0.3423 target_work(ls_wunit_k1) = 0.128 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3423 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 moved from start: 0.2446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 3856 Z= 0.172 Angle : 0.553 7.113 5239 Z= 0.286 Chirality : 0.044 0.150 604 Planarity : 0.003 0.033 652 Dihedral : 5.112 36.119 530 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.96 % Favored : 93.04 % Rotamer: Outliers : 3.61 % Allowed : 21.45 % Favored : 74.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.22 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.67 (0.38), residues: 474 helix: -2.68 (0.48), residues: 92 sheet: -0.68 (0.44), residues: 150 loop : -2.10 (0.39), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 10 TYR 0.015 0.001 TYR A 213 PHE 0.009 0.001 PHE B 89 TRP 0.011 0.001 TRP D 33 HIS 0.003 0.001 HIS A 192 Details of bonding type rmsd covalent geometry : bond 0.00416 ( 3854) covalent geometry : angle 0.55252 ( 5235) SS BOND : bond 0.00820 ( 2) SS BOND : angle 1.13354 ( 4) hydrogen bonds : bond 0.02936 ( 99) hydrogen bonds : angle 4.99013 ( 240) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 948 Ramachandran restraints generated. 474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 948 Ramachandran restraints generated. 474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 64 time to evaluate : 0.099 Fit side-chains REVERT: A 179 MET cc_start: 0.8273 (OUTLIER) cc_final: 0.7565 (ttt) REVERT: B 78 ARG cc_start: 0.7756 (mmt180) cc_final: 0.6807 (mmm160) REVERT: D 10 ARG cc_start: 0.7351 (mtt180) cc_final: 0.7106 (ptm-80) REVERT: D 29 LEU cc_start: 0.8798 (OUTLIER) cc_final: 0.8486 (pp) outliers start: 15 outliers final: 11 residues processed: 73 average time/residue: 0.0914 time to fit residues: 7.9097 Evaluate side-chains 76 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 63 time to evaluate : 0.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 CYS Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 179 MET Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain B residue 117 SER Chi-restraints excluded: chain D residue 2 GLN Chi-restraints excluded: chain D residue 4 VAL Chi-restraints excluded: chain D residue 6 GLU Chi-restraints excluded: chain D residue 29 LEU Chi-restraints excluded: chain D residue 64 LYS Chi-restraints excluded: chain D residue 113 THR Chi-restraints excluded: chain G residue 101 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 27 optimal weight: 0.9990 chunk 15 optimal weight: 0.2980 chunk 19 optimal weight: 3.9990 chunk 20 optimal weight: 1.9990 chunk 3 optimal weight: 0.0040 chunk 32 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 11 optimal weight: 0.9990 chunk 2 optimal weight: 0.5980 chunk 44 optimal weight: 0.5980 chunk 4 optimal weight: 0.0070 overall best weight: 0.3010 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 81 ASN B 84 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.142744 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.116920 restraints weight = 5209.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.120592 restraints weight = 3097.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.122930 restraints weight = 2217.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.124713 restraints weight = 1776.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.125891 restraints weight = 1509.264| |-----------------------------------------------------------------------------| r_work (final): 0.3412 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3454 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3454 r_free = 0.3454 target_work(ls_wunit_k1) = 0.130 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3454 r_free = 0.3454 target_work(ls_wunit_k1) = 0.130 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3454 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8044 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 0.021 3856 Z= 0.099 Angle : 0.511 6.445 5239 Z= 0.262 Chirality : 0.042 0.138 604 Planarity : 0.003 0.032 652 Dihedral : 4.726 30.709 530 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 3.61 % Allowed : 21.20 % Favored : 75.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.22 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.42 (0.39), residues: 474 helix: -2.45 (0.51), residues: 92 sheet: -0.55 (0.45), residues: 150 loop : -1.94 (0.40), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 95 TYR 0.008 0.001 TYR G 49 PHE 0.007 0.001 PHE A 177 TRP 0.009 0.001 TRP D 33 HIS 0.003 0.001 HIS A 26 Details of bonding type rmsd covalent geometry : bond 0.00230 ( 3854) covalent geometry : angle 0.51018 ( 5235) SS BOND : bond 0.00666 ( 2) SS BOND : angle 1.11283 ( 4) hydrogen bonds : bond 0.02556 ( 99) hydrogen bonds : angle 4.78747 ( 240) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 948 Ramachandran restraints generated. 474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 948 Ramachandran restraints generated. 474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 62 time to evaluate : 0.150 Fit side-chains REVERT: A 179 MET cc_start: 0.8239 (OUTLIER) cc_final: 0.7550 (ttt) REVERT: A 232 PHE cc_start: 0.7825 (OUTLIER) cc_final: 0.7467 (t80) REVERT: A 233 VAL cc_start: 0.8608 (OUTLIER) cc_final: 0.8406 (p) REVERT: A 248 ASP cc_start: 0.8049 (m-30) cc_final: 0.7665 (t70) REVERT: B 78 ARG cc_start: 0.7703 (mmt180) cc_final: 0.6775 (mmm160) REVERT: D 29 LEU cc_start: 0.8777 (OUTLIER) cc_final: 0.8482 (pp) outliers start: 15 outliers final: 10 residues processed: 71 average time/residue: 0.0875 time to fit residues: 7.3483 Evaluate side-chains 75 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 61 time to evaluate : 0.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 CYS Chi-restraints excluded: chain A residue 179 MET Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 232 PHE Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain D residue 2 GLN Chi-restraints excluded: chain D residue 4 VAL Chi-restraints excluded: chain D residue 6 GLU Chi-restraints excluded: chain D residue 29 LEU Chi-restraints excluded: chain D residue 64 LYS Chi-restraints excluded: chain D residue 113 THR Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 101 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 38 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 chunk 37 optimal weight: 0.8980 chunk 7 optimal weight: 0.0980 chunk 26 optimal weight: 0.0970 chunk 28 optimal weight: 0.9990 chunk 33 optimal weight: 0.7980 chunk 13 optimal weight: 1.9990 chunk 8 optimal weight: 0.0980 chunk 30 optimal weight: 0.5980 chunk 18 optimal weight: 0.9990 overall best weight: 0.3378 ------------------------------------------------------------------------------- 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 = 0.3650 r_free = 0.3650 target = 0.147949 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.122060 restraints weight = 5271.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.125903 restraints weight = 3066.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.128340 restraints weight = 2175.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.130125 restraints weight = 1730.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.131207 restraints weight = 1467.798| |-----------------------------------------------------------------------------| r_work (final): 0.3431 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3413 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3413 r_free = 0.3413 target_work(ls_wunit_k1) = 0.127 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3413 r_free = 0.3413 target_work(ls_wunit_k1) = 0.127 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3413 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 moved from start: 0.2789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 3856 Z= 0.105 Angle : 0.502 6.394 5239 Z= 0.258 Chirality : 0.042 0.142 604 Planarity : 0.003 0.031 652 Dihedral : 4.581 29.391 530 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 3.61 % Allowed : 20.96 % Favored : 75.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.22 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.31 (0.39), residues: 474 helix: -2.31 (0.52), residues: 92 sheet: -0.46 (0.45), residues: 150 loop : -1.91 (0.40), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 95 TYR 0.008 0.001 TYR G 49 PHE 0.007 0.001 PHE A 177 TRP 0.010 0.001 TRP D 33 HIS 0.002 0.001 HIS A 26 Details of bonding type rmsd covalent geometry : bond 0.00249 ( 3854) covalent geometry : angle 0.50168 ( 5235) SS BOND : bond 0.00671 ( 2) SS BOND : angle 1.10499 ( 4) hydrogen bonds : bond 0.02541 ( 99) hydrogen bonds : angle 4.67624 ( 240) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 948 Ramachandran restraints generated. 474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 948 Ramachandran restraints generated. 474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 63 time to evaluate : 0.156 Fit side-chains REVERT: A 179 MET cc_start: 0.8229 (OUTLIER) cc_final: 0.7543 (ttt) REVERT: A 232 PHE cc_start: 0.7863 (OUTLIER) cc_final: 0.7502 (t80) REVERT: A 248 ASP cc_start: 0.8010 (m-30) cc_final: 0.7645 (t70) REVERT: B 78 ARG cc_start: 0.7695 (mmt180) cc_final: 0.6729 (mmm160) REVERT: D 29 LEU cc_start: 0.8765 (OUTLIER) cc_final: 0.8437 (pp) outliers start: 15 outliers final: 10 residues processed: 72 average time/residue: 0.0920 time to fit residues: 7.7454 Evaluate side-chains 74 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 61 time to evaluate : 0.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 CYS Chi-restraints excluded: chain A residue 179 MET Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 232 PHE Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain D residue 2 GLN Chi-restraints excluded: chain D residue 4 VAL Chi-restraints excluded: chain D residue 6 GLU Chi-restraints excluded: chain D residue 29 LEU Chi-restraints excluded: chain D residue 64 LYS Chi-restraints excluded: chain D residue 113 THR Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 101 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 0 optimal weight: 2.9990 chunk 16 optimal weight: 0.3980 chunk 13 optimal weight: 0.3980 chunk 28 optimal weight: 0.7980 chunk 9 optimal weight: 0.9980 chunk 10 optimal weight: 1.9990 chunk 24 optimal weight: 0.9980 chunk 34 optimal weight: 0.3980 chunk 29 optimal weight: 0.3980 chunk 7 optimal weight: 0.0030 chunk 33 optimal weight: 0.7980 overall best weight: 0.3190 ------------------------------------------------------------------------------- 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 = 0.3578 r_free = 0.3578 target = 0.142683 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.116757 restraints weight = 5193.871| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.120376 restraints weight = 3103.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.122803 restraints weight = 2235.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.124445 restraints weight = 1784.750| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.125602 restraints weight = 1523.985| |-----------------------------------------------------------------------------| r_work (final): 0.3417 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3418 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3418 r_free = 0.3418 target_work(ls_wunit_k1) = 0.128 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3418 r_free = 0.3418 target_work(ls_wunit_k1) = 0.128 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3418 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.2875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.120 3856 Z= 0.108 Angle : 0.510 6.226 5239 Z= 0.261 Chirality : 0.042 0.198 604 Planarity : 0.003 0.032 652 Dihedral : 4.480 28.522 530 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 2.89 % Allowed : 21.93 % Favored : 75.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.22 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.23 (0.39), residues: 474 helix: -2.24 (0.52), residues: 92 sheet: -0.40 (0.45), residues: 150 loop : -1.86 (0.40), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 102 TYR 0.008 0.001 TYR G 49 PHE 0.007 0.001 PHE A 177 TRP 0.009 0.001 TRP D 33 HIS 0.003 0.001 HIS A 234 Details of bonding type rmsd covalent geometry : bond 0.00305 ( 3854) covalent geometry : angle 0.50916 ( 5235) SS BOND : bond 0.00656 ( 2) SS BOND : angle 1.03219 ( 4) hydrogen bonds : bond 0.02495 ( 99) hydrogen bonds : angle 4.59163 ( 240) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1032.71 seconds wall clock time: 18 minutes 26.98 seconds (1106.98 seconds total)