Starting phenix.real_space_refine on Wed Jun 4 18:18:02 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7yp1_33992/06_2025/7yp1_33992.cif Found real_map, /net/cci-nas-00/data/ceres_data/7yp1_33992/06_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_33992/06_2025/7yp1_33992.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7yp1_33992/06_2025/7yp1_33992.map" model { file = "/net/cci-nas-00/data/ceres_data/7yp1_33992/06_2025/7yp1_33992.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7yp1_33992/06_2025/7yp1_33992.cif" } resolution = 3.54 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= 0.000 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): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 3.57, per 1000 atoms: 0.95 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: 0.85 Conformation dependent library (CDL) restraints added in 456.5 milliseconds 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: 0.47 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: 0.85 Time building geometry restraints manager: 1.02 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: 3.670 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.170 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 13.950 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.640 ------------------------------------------------------------------------------- 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 (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: -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 TRP 0.016 0.003 TRP D 33 HIS 0.008 0.002 HIS A 192 PHE 0.021 0.003 PHE A 177 TYR 0.017 0.002 TYR A 132 ARG 0.006 0.001 ARG D 95 Details of bonding type rmsd hydrogen bonds : bond 0.28118 ( 99) hydrogen bonds : angle 10.29860 ( 240) SS BOND : bond 0.00830 ( 2) SS BOND : angle 1.50343 ( 4) covalent geometry : bond 0.01047 ( 3854) covalent geometry : angle 1.05487 ( 5235) *********************** 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 : 0.422 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: 0.2234 time to fit residues: 19.4676 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 : 0.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 39 optimal weight: 0.6980 chunk 35 optimal weight: 0.5980 chunk 19 optimal weight: 3.9990 chunk 12 optimal weight: 0.5980 chunk 24 optimal weight: 0.2980 chunk 36 optimal weight: 1.9990 chunk 14 optimal weight: 0.4980 chunk 22 optimal weight: 0.9990 chunk 27 optimal weight: 0.4980 chunk 42 optimal weight: 0.9990 chunk 23 optimal weight: 1.9990 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.144024 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.117767 restraints weight = 5114.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.121573 restraints weight = 3011.070| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.124069 restraints weight = 2155.659| |-----------------------------------------------------------------------------| r_work (final): 0.3365 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3384 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3384 r_free = 0.3384 target_work(ls_wunit_k1) = 0.125 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3365 r_free = 0.3365 target_work(ls_wunit_k1) = 0.123 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3365 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.1401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 3856 Z= 0.155 Angle : 0.606 6.950 5239 Z= 0.320 Chirality : 0.045 0.154 604 Planarity : 0.005 0.041 652 Dihedral : 5.917 44.348 530 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.54 % Favored : 93.46 % Rotamer: Outliers : 1.69 % Allowed : 16.39 % Favored : 81.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.22 % 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: -4.27 (0.33), residues: 474 helix: -4.22 (0.29), residues: 88 sheet: -1.75 (0.43), residues: 154 loop : -3.01 (0.33), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 33 HIS 0.003 0.001 HIS A 192 PHE 0.007 0.001 PHE B 89 TYR 0.010 0.001 TYR D 47 ARG 0.002 0.000 ARG A 152 Details of bonding type rmsd hydrogen bonds : bond 0.04493 ( 99) hydrogen bonds : angle 6.48017 ( 240) SS BOND : bond 0.00792 ( 2) SS BOND : angle 0.91127 ( 4) covalent geometry : bond 0.00363 ( 3854) covalent geometry : angle 0.60581 ( 5235) *********************** 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 74 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 67 time to evaluate : 0.368 Fit side-chains REVERT: B 78 ARG cc_start: 0.7706 (mmt180) cc_final: 0.6703 (mmm160) outliers start: 7 outliers final: 5 residues processed: 72 average time/residue: 0.2064 time to fit residues: 17.5651 Evaluate side-chains 67 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 62 time to evaluate : 0.399 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 31 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 14 optimal weight: 0.4980 chunk 21 optimal weight: 0.8980 chunk 24 optimal weight: 0.9990 chunk 42 optimal weight: 3.9990 chunk 23 optimal weight: 1.9990 chunk 11 optimal weight: 0.9990 chunk 40 optimal weight: 0.4980 chunk 36 optimal weight: 0.9980 overall best weight: 0.7782 ------------------------------------------------------------------------------- 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 = 0.3539 r_free = 0.3539 target = 0.139317 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.112936 restraints weight = 5134.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.116662 restraints weight = 3038.187| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.119026 restraints weight = 2174.458| |-----------------------------------------------------------------------------| r_work (final): 0.3313 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3356 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3356 r_free = 0.3356 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 = 0.3354 r_free = 0.3354 target_work(ls_wunit_k1) = 0.123 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3354 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.1711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.030 3856 Z= 0.205 Angle : 0.600 6.979 5239 Z= 0.315 Chirality : 0.045 0.157 604 Planarity : 0.004 0.032 652 Dihedral : 5.659 39.787 530 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.59 % Favored : 92.41 % Rotamer: Outliers : 4.34 % Allowed : 17.83 % Favored : 77.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.22 % 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: -3.78 (0.35), residues: 474 helix: -3.63 (0.38), residues: 90 sheet: -1.51 (0.43), residues: 151 loop : -2.71 (0.36), residues: 233 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 33 HIS 0.004 0.001 HIS A 192 PHE 0.011 0.001 PHE A 177 TYR 0.012 0.001 TYR G 92 ARG 0.002 0.000 ARG A 152 Details of bonding type rmsd hydrogen bonds : bond 0.03822 ( 99) hydrogen bonds : angle 5.78845 ( 240) SS BOND : bond 0.00792 ( 2) SS BOND : angle 0.98556 ( 4) covalent geometry : bond 0.00491 ( 3854) covalent geometry : angle 0.59942 ( 5235) *********************** 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 83 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 65 time to evaluate : 0.493 Fit side-chains REVERT: A 179 MET cc_start: 0.8305 (OUTLIER) cc_final: 0.7592 (ttt) REVERT: A 184 ARG cc_start: 0.6933 (ttp80) cc_final: 0.6583 (mmt180) REVERT: B 78 ARG cc_start: 0.7707 (mmt180) cc_final: 0.6675 (mmm160) REVERT: D 10 ARG cc_start: 0.7374 (mtt180) cc_final: 0.7063 (ptm-80) REVERT: D 29 LEU cc_start: 0.8811 (OUTLIER) cc_final: 0.8465 (pp) REVERT: D 80 ILE cc_start: 0.8189 (OUTLIER) cc_final: 0.7944 (mt) outliers start: 18 outliers final: 9 residues processed: 79 average time/residue: 0.2186 time to fit residues: 20.3794 Evaluate side-chains 75 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 63 time to evaluate : 0.394 ------------------------------------------------------------------------------- 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 D residue 2 GLN Chi-restraints excluded: chain D residue 29 LEU Chi-restraints excluded: chain D residue 64 LYS Chi-restraints excluded: chain D residue 80 ILE Chi-restraints excluded: chain D residue 81 THR Chi-restraints excluded: chain D residue 84 THR 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 39 optimal weight: 1.9990 chunk 43 optimal weight: 0.2980 chunk 44 optimal weight: 0.5980 chunk 17 optimal weight: 1.9990 chunk 11 optimal weight: 0.9980 chunk 29 optimal weight: 0.9990 chunk 1 optimal weight: 0.2980 chunk 46 optimal weight: 0.5980 chunk 12 optimal weight: 0.6980 chunk 20 optimal weight: 2.9990 chunk 25 optimal weight: 0.9990 overall best weight: 0.4980 ------------------------------------------------------------------------------- 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 = 0.3489 r_free = 0.3489 target = 0.136507 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.111647 restraints weight = 5232.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.114912 restraints weight = 3316.140| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.117052 restraints weight = 2447.964| |-----------------------------------------------------------------------------| r_work (final): 0.3258 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3282 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3282 r_free = 0.3282 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3282 r_free = 0.3282 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3282 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.1938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3856 Z= 0.139 Angle : 0.537 6.383 5239 Z= 0.282 Chirality : 0.043 0.146 604 Planarity : 0.004 0.034 652 Dihedral : 5.307 35.566 530 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer: Outliers : 2.89 % Allowed : 20.96 % 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 (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: -3.38 (0.36), residues: 474 helix: -3.26 (0.43), residues: 91 sheet: -1.21 (0.44), residues: 155 loop : -2.51 (0.37), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 33 HIS 0.003 0.001 HIS A 26 PHE 0.008 0.001 PHE A 177 TYR 0.009 0.001 TYR D 47 ARG 0.001 0.000 ARG D 10 Details of bonding type rmsd hydrogen bonds : bond 0.03130 ( 99) hydrogen bonds : angle 5.42504 ( 240) SS BOND : bond 0.00670 ( 2) SS BOND : angle 1.01134 ( 4) covalent geometry : bond 0.00332 ( 3854) covalent geometry : angle 0.53681 ( 5235) *********************** 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 81 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 69 time to evaluate : 0.554 Fit side-chains REVERT: A 179 MET cc_start: 0.8367 (OUTLIER) cc_final: 0.7574 (ttt) REVERT: A 184 ARG cc_start: 0.6977 (ttp80) cc_final: 0.6499 (mmt180) REVERT: B 78 ARG cc_start: 0.7666 (mmt180) cc_final: 0.6589 (mmm160) REVERT: D 10 ARG cc_start: 0.7423 (mtt180) cc_final: 0.7025 (ptm-80) REVERT: D 80 ILE cc_start: 0.8053 (OUTLIER) cc_final: 0.7816 (mt) outliers start: 12 outliers final: 9 residues processed: 77 average time/residue: 0.2148 time to fit residues: 19.6837 Evaluate side-chains 74 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 63 time to evaluate : 0.395 ------------------------------------------------------------------------------- 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 D residue 4 VAL Chi-restraints excluded: chain D residue 6 GLU Chi-restraints excluded: chain D residue 64 LYS Chi-restraints excluded: chain D residue 80 ILE 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 8 optimal weight: 0.9990 chunk 5 optimal weight: 1.9990 chunk 46 optimal weight: 0.6980 chunk 33 optimal weight: 0.6980 chunk 19 optimal weight: 4.9990 chunk 28 optimal weight: 1.9990 chunk 27 optimal weight: 0.6980 chunk 6 optimal weight: 0.8980 chunk 42 optimal weight: 3.9990 chunk 10 optimal weight: 1.9990 chunk 22 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 = 0.3455 r_free = 0.3455 target = 0.133892 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.108684 restraints weight = 5324.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.111912 restraints weight = 3358.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.114164 restraints weight = 2478.001| |-----------------------------------------------------------------------------| r_work (final): 0.3212 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3199 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3199 r_free = 0.3199 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3199 r_free = 0.3199 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3199 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 moved from start: 0.2019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 3856 Z= 0.205 Angle : 0.579 6.620 5239 Z= 0.302 Chirality : 0.045 0.155 604 Planarity : 0.004 0.031 652 Dihedral : 5.431 37.890 530 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.59 % Favored : 92.41 % Rotamer: Outliers : 4.10 % Allowed : 20.48 % 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 (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: -3.19 (0.37), residues: 474 helix: -3.06 (0.46), residues: 90 sheet: -1.05 (0.44), residues: 155 loop : -2.45 (0.38), residues: 229 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 33 HIS 0.003 0.001 HIS A 26 PHE 0.010 0.001 PHE B 89 TYR 0.011 0.001 TYR D 47 ARG 0.002 0.000 ARG D 10 Details of bonding type rmsd hydrogen bonds : bond 0.03390 ( 99) hydrogen bonds : angle 5.39714 ( 240) SS BOND : bond 0.00768 ( 2) SS BOND : angle 0.87012 ( 4) covalent geometry : bond 0.00494 ( 3854) covalent geometry : angle 0.57870 ( 5235) *********************** 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 83 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 66 time to evaluate : 0.425 Fit side-chains REVERT: A 137 MET cc_start: 0.8954 (tpt) cc_final: 0.8658 (tpt) REVERT: A 179 MET cc_start: 0.8403 (OUTLIER) cc_final: 0.7578 (ttt) REVERT: A 184 ARG cc_start: 0.6991 (ttp80) cc_final: 0.6596 (mmt180) REVERT: B 78 ARG cc_start: 0.7632 (mmt180) cc_final: 0.6469 (mmm160) REVERT: D 10 ARG cc_start: 0.7511 (mtt180) cc_final: 0.6946 (ptm-80) REVERT: D 29 LEU cc_start: 0.8699 (OUTLIER) cc_final: 0.8353 (pp) REVERT: D 80 ILE cc_start: 0.7935 (OUTLIER) cc_final: 0.7680 (mt) outliers start: 17 outliers final: 10 residues processed: 78 average time/residue: 0.1934 time to fit residues: 18.1339 Evaluate side-chains 78 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 65 time to evaluate : 0.431 ------------------------------------------------------------------------------- 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 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 80 ILE Chi-restraints excluded: chain D residue 81 THR 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 39 optimal weight: 0.6980 chunk 40 optimal weight: 0.0770 chunk 15 optimal weight: 0.1980 chunk 31 optimal weight: 0.6980 chunk 9 optimal weight: 0.9980 chunk 35 optimal weight: 0.7980 chunk 7 optimal weight: 0.1980 chunk 11 optimal weight: 0.4980 chunk 3 optimal weight: 1.9990 chunk 44 optimal weight: 0.7980 chunk 45 optimal weight: 0.6980 overall best weight: 0.3338 ------------------------------------------------------------------------------- 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 = 0.3491 r_free = 0.3491 target = 0.136687 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.112170 restraints weight = 5236.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.115314 restraints weight = 3280.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.117674 restraints weight = 2417.523| |-----------------------------------------------------------------------------| r_work (final): 0.3284 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3306 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3306 r_free = 0.3306 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3306 r_free = 0.3306 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3306 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 moved from start: 0.2257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3856 Z= 0.112 Angle : 0.514 7.259 5239 Z= 0.267 Chirality : 0.042 0.142 604 Planarity : 0.004 0.033 652 Dihedral : 4.959 31.414 530 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 3.13 % Allowed : 22.89 % Favored : 73.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.22 % 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: 474 helix: -2.82 (0.48), residues: 90 sheet: -0.82 (0.44), residues: 155 loop : -2.33 (0.39), residues: 229 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 33 HIS 0.002 0.001 HIS A 26 PHE 0.007 0.001 PHE A 177 TYR 0.011 0.001 TYR A 213 ARG 0.001 0.000 ARG D 95 Details of bonding type rmsd hydrogen bonds : bond 0.02839 ( 99) hydrogen bonds : angle 5.08474 ( 240) SS BOND : bond 0.00720 ( 2) SS BOND : angle 1.06053 ( 4) covalent geometry : bond 0.00265 ( 3854) covalent geometry : angle 0.51374 ( 5235) *********************** 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 79 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 66 time to evaluate : 0.368 Fit side-chains REVERT: A 179 MET cc_start: 0.8318 (OUTLIER) cc_final: 0.7544 (ttt) REVERT: A 184 ARG cc_start: 0.6924 (ttp80) cc_final: 0.6555 (mmt180) REVERT: B 78 ARG cc_start: 0.7679 (mmt180) cc_final: 0.6614 (mmm160) REVERT: D 10 ARG cc_start: 0.7400 (mtt180) cc_final: 0.6987 (ptm-80) REVERT: D 29 LEU cc_start: 0.8729 (OUTLIER) cc_final: 0.8398 (pp) REVERT: D 80 ILE cc_start: 0.8006 (OUTLIER) cc_final: 0.7756 (mt) outliers start: 13 outliers final: 8 residues processed: 74 average time/residue: 0.2089 time to fit residues: 18.3098 Evaluate side-chains 75 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 64 time to evaluate : 0.399 ------------------------------------------------------------------------------- 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 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 80 ILE Chi-restraints excluded: chain D residue 113 THR Chi-restraints excluded: chain G residue 11 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 2 optimal weight: 0.0570 chunk 30 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 18 optimal weight: 0.9980 chunk 33 optimal weight: 1.9990 chunk 29 optimal weight: 0.2980 chunk 44 optimal weight: 0.0870 chunk 19 optimal weight: 0.0670 chunk 42 optimal weight: 3.9990 chunk 5 optimal weight: 0.9990 overall best weight: 0.3014 ------------------------------------------------------------------------------- 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 = 0.3493 r_free = 0.3493 target = 0.136877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.112326 restraints weight = 5220.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.115617 restraints weight = 3276.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.117740 restraints weight = 2411.147| |-----------------------------------------------------------------------------| r_work (final): 0.3294 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3347 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3347 r_free = 0.3347 target_work(ls_wunit_k1) = 0.123 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3346 r_free = 0.3346 target_work(ls_wunit_k1) = 0.123 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3346 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 moved from start: 0.2395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 3856 Z= 0.101 Angle : 0.496 6.656 5239 Z= 0.258 Chirality : 0.042 0.141 604 Planarity : 0.003 0.029 652 Dihedral : 4.751 29.210 530 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 3.86 % Allowed : 22.17 % Favored : 73.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.22 % 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: -2.77 (0.38), residues: 474 helix: -2.66 (0.49), residues: 91 sheet: -0.71 (0.45), residues: 149 loop : -2.25 (0.39), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 33 HIS 0.002 0.001 HIS A 26 PHE 0.005 0.001 PHE D 105 TYR 0.008 0.001 TYR D 47 ARG 0.001 0.000 ARG D 95 Details of bonding type rmsd hydrogen bonds : bond 0.02745 ( 99) hydrogen bonds : angle 4.91843 ( 240) SS BOND : bond 0.00729 ( 2) SS BOND : angle 1.21809 ( 4) covalent geometry : bond 0.00238 ( 3854) covalent geometry : angle 0.49478 ( 5235) *********************** 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 83 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 67 time to evaluate : 0.394 Fit side-chains REVERT: A 179 MET cc_start: 0.8279 (OUTLIER) cc_final: 0.7490 (ttt) REVERT: A 184 ARG cc_start: 0.6911 (ttp80) cc_final: 0.6577 (mmt180) REVERT: A 232 PHE cc_start: 0.7729 (OUTLIER) cc_final: 0.7383 (t80) REVERT: A 248 ASP cc_start: 0.8005 (m-30) cc_final: 0.7475 (t70) REVERT: B 78 ARG cc_start: 0.7701 (mmt180) cc_final: 0.6647 (mmm160) REVERT: D 10 ARG cc_start: 0.7379 (mtt180) cc_final: 0.7050 (ptm-80) REVERT: D 29 LEU cc_start: 0.8748 (OUTLIER) cc_final: 0.8434 (pp) REVERT: D 80 ILE cc_start: 0.8002 (OUTLIER) cc_final: 0.7759 (mt) outliers start: 16 outliers final: 9 residues processed: 78 average time/residue: 0.2064 time to fit residues: 19.0659 Evaluate side-chains 78 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 65 time to evaluate : 0.389 ------------------------------------------------------------------------------- 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 80 ILE Chi-restraints excluded: chain D residue 113 THR Chi-restraints excluded: chain G residue 11 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 21 optimal weight: 1.9990 chunk 29 optimal weight: 0.5980 chunk 16 optimal weight: 0.8980 chunk 40 optimal weight: 0.9980 chunk 25 optimal weight: 1.9990 chunk 27 optimal weight: 0.5980 chunk 19 optimal weight: 3.9990 chunk 36 optimal weight: 1.9990 chunk 45 optimal weight: 0.8980 chunk 37 optimal weight: 2.9990 chunk 41 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.3586 r_free = 0.3586 target = 0.142481 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.116438 restraints weight = 5274.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.120182 restraints weight = 3100.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.122625 restraints weight = 2207.592| |-----------------------------------------------------------------------------| r_work (final): 0.3292 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3366 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3366 r_free = 0.3366 target_work(ls_wunit_k1) = 0.123 | | 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) = 0.123 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3366 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.2331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.118 3856 Z= 0.199 Angle : 0.575 7.274 5239 Z= 0.300 Chirality : 0.045 0.199 604 Planarity : 0.003 0.031 652 Dihedral : 5.127 35.752 530 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.75 % Favored : 93.25 % Rotamer: Outliers : 4.10 % Allowed : 21.69 % Favored : 74.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.22 % 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: -2.80 (0.38), residues: 474 helix: -2.68 (0.48), residues: 91 sheet: -0.72 (0.45), residues: 149 loop : -2.27 (0.39), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 33 HIS 0.002 0.001 HIS A 192 PHE 0.010 0.001 PHE B 89 TYR 0.012 0.001 TYR A 213 ARG 0.002 0.000 ARG A 152 Details of bonding type rmsd hydrogen bonds : bond 0.03175 ( 99) hydrogen bonds : angle 5.04256 ( 240) SS BOND : bond 0.00871 ( 2) SS BOND : angle 1.13491 ( 4) covalent geometry : bond 0.00509 ( 3854) covalent geometry : angle 0.57473 ( 5235) *********************** 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 82 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 65 time to evaluate : 0.412 Fit side-chains REVERT: A 179 MET cc_start: 0.8286 (OUTLIER) cc_final: 0.7584 (ttt) REVERT: A 232 PHE cc_start: 0.7845 (OUTLIER) cc_final: 0.7479 (t80) REVERT: B 78 ARG cc_start: 0.7769 (mmt180) cc_final: 0.6817 (mmm160) REVERT: D 10 ARG cc_start: 0.7392 (mtt180) cc_final: 0.7080 (ptm-80) REVERT: D 29 LEU cc_start: 0.8803 (OUTLIER) cc_final: 0.8491 (pp) REVERT: D 80 ILE cc_start: 0.8145 (OUTLIER) cc_final: 0.7882 (mt) outliers start: 17 outliers final: 11 residues processed: 76 average time/residue: 0.2083 time to fit residues: 18.7748 Evaluate side-chains 80 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 65 time to evaluate : 0.402 ------------------------------------------------------------------------------- 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 215 SER 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 80 ILE Chi-restraints excluded: chain D residue 113 THR Chi-restraints excluded: chain G residue 11 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 23 optimal weight: 3.9990 chunk 18 optimal weight: 2.9990 chunk 45 optimal weight: 0.5980 chunk 31 optimal weight: 1.9990 chunk 5 optimal weight: 0.9990 chunk 32 optimal weight: 0.8980 chunk 10 optimal weight: 1.9990 chunk 19 optimal weight: 0.0040 chunk 13 optimal weight: 0.9980 chunk 21 optimal weight: 0.6980 chunk 36 optimal weight: 1.9990 overall best weight: 0.6392 ------------------------------------------------------------------------------- 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 = 0.3487 r_free = 0.3487 target = 0.135965 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.110116 restraints weight = 5160.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.113584 restraints weight = 3129.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.115976 restraints weight = 2263.937| |-----------------------------------------------------------------------------| r_work (final): 0.3357 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3391 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3391 r_free = 0.3391 target_work(ls_wunit_k1) = 0.125 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3391 r_free = 0.3391 target_work(ls_wunit_k1) = 0.125 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3391 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.2455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 3856 Z= 0.169 Angle : 0.550 7.168 5239 Z= 0.288 Chirality : 0.044 0.148 604 Planarity : 0.003 0.030 652 Dihedral : 5.105 34.629 530 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.91 % Favored : 94.09 % Rotamer: Outliers : 4.34 % Allowed : 21.93 % Favored : 73.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.22 % 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: -2.69 (0.38), residues: 474 helix: -2.60 (0.49), residues: 91 sheet: -0.68 (0.45), residues: 149 loop : -2.18 (0.39), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 33 HIS 0.002 0.001 HIS A 26 PHE 0.012 0.001 PHE A 177 TYR 0.014 0.001 TYR A 213 ARG 0.002 0.000 ARG D 10 Details of bonding type rmsd hydrogen bonds : bond 0.03026 ( 99) hydrogen bonds : angle 5.00015 ( 240) SS BOND : bond 0.00829 ( 2) SS BOND : angle 1.11549 ( 4) covalent geometry : bond 0.00412 ( 3854) covalent geometry : angle 0.54902 ( 5235) *********************** 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 81 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 63 time to evaluate : 0.416 Fit side-chains REVERT: A 179 MET cc_start: 0.8243 (OUTLIER) cc_final: 0.7608 (ttt) REVERT: A 232 PHE cc_start: 0.7913 (OUTLIER) cc_final: 0.7517 (t80) REVERT: B 78 ARG cc_start: 0.7778 (mmt180) cc_final: 0.6843 (mmm160) REVERT: D 10 ARG cc_start: 0.7408 (mtt180) cc_final: 0.7081 (ptm-80) REVERT: D 29 LEU cc_start: 0.8804 (OUTLIER) cc_final: 0.8509 (pp) REVERT: D 80 ILE cc_start: 0.8175 (OUTLIER) cc_final: 0.7900 (mt) outliers start: 18 outliers final: 12 residues processed: 76 average time/residue: 0.2026 time to fit residues: 18.3157 Evaluate side-chains 78 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 62 time to evaluate : 0.412 ------------------------------------------------------------------------------- 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 215 SER Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 231 THR 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 80 ILE Chi-restraints excluded: chain D residue 113 THR Chi-restraints excluded: chain G residue 11 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 23 optimal weight: 3.9990 chunk 32 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 26 optimal weight: 0.4980 chunk 22 optimal weight: 0.9990 chunk 2 optimal weight: 0.0060 chunk 27 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 15 optimal weight: 0.0970 overall best weight: 0.7198 ------------------------------------------------------------------------------- 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 = 0.3519 r_free = 0.3519 target = 0.137872 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.111312 restraints weight = 5274.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.115057 restraints weight = 3084.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.117605 restraints weight = 2188.891| |-----------------------------------------------------------------------------| r_work (final): 0.3378 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3324 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3324 r_free = 0.3324 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3324 r_free = 0.3324 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3324 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 moved from start: 0.2477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.096 3856 Z= 0.189 Angle : 0.569 7.315 5239 Z= 0.298 Chirality : 0.044 0.151 604 Planarity : 0.003 0.030 652 Dihedral : 5.194 35.808 530 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.96 % Favored : 93.04 % Rotamer: Outliers : 4.10 % Allowed : 22.41 % Favored : 73.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.22 % 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: -2.73 (0.38), residues: 474 helix: -2.63 (0.49), residues: 92 sheet: -0.68 (0.45), residues: 149 loop : -2.20 (0.39), residues: 233 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 33 HIS 0.002 0.001 HIS A 192 PHE 0.014 0.001 PHE A 177 TYR 0.010 0.001 TYR A 213 ARG 0.002 0.000 ARG D 10 Details of bonding type rmsd hydrogen bonds : bond 0.03123 ( 99) hydrogen bonds : angle 5.02353 ( 240) SS BOND : bond 0.00845 ( 2) SS BOND : angle 1.13904 ( 4) covalent geometry : bond 0.00476 ( 3854) covalent geometry : angle 0.56851 ( 5235) ********************** 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 79 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 62 time to evaluate : 0.435 Fit side-chains REVERT: A 179 MET cc_start: 0.8275 (OUTLIER) cc_final: 0.7597 (ttt) REVERT: A 232 PHE cc_start: 0.7942 (OUTLIER) cc_final: 0.7546 (t80) REVERT: B 78 ARG cc_start: 0.7770 (mmt180) cc_final: 0.6775 (mmm160) REVERT: D 10 ARG cc_start: 0.7430 (mtt180) cc_final: 0.7050 (ptm-80) REVERT: D 29 LEU cc_start: 0.8803 (OUTLIER) cc_final: 0.8513 (pp) REVERT: D 80 ILE cc_start: 0.8171 (OUTLIER) cc_final: 0.7909 (mt) outliers start: 17 outliers final: 11 residues processed: 74 average time/residue: 0.1951 time to fit residues: 17.4034 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 : 0.430 ------------------------------------------------------------------------------- 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 215 SER Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 231 THR 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 29 LEU Chi-restraints excluded: chain D residue 64 LYS Chi-restraints excluded: chain D residue 80 ILE Chi-restraints excluded: chain D residue 113 THR Chi-restraints excluded: chain G residue 11 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 42 optimal weight: 1.9990 chunk 7 optimal weight: 0.9980 chunk 40 optimal weight: 0.0470 chunk 46 optimal weight: 0.8980 chunk 9 optimal weight: 0.9980 chunk 32 optimal weight: 2.9990 chunk 23 optimal weight: 3.9990 chunk 25 optimal weight: 0.6980 chunk 43 optimal weight: 0.8980 chunk 37 optimal weight: 1.9990 chunk 28 optimal weight: 0.6980 overall best weight: 0.6478 ------------------------------------------------------------------------------- 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 = 0.3522 r_free = 0.3522 target = 0.138034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.111668 restraints weight = 5204.149| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.115387 restraints weight = 3040.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.117850 restraints weight = 2167.362| |-----------------------------------------------------------------------------| r_work (final): 0.3361 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3358 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3358 r_free = 0.3358 target_work(ls_wunit_k1) = 0.123 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3358 r_free = 0.3358 target_work(ls_wunit_k1) = 0.123 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3358 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8109 moved from start: 0.2518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.101 3856 Z= 0.174 Angle : 0.560 7.095 5239 Z= 0.292 Chirality : 0.044 0.149 604 Planarity : 0.003 0.030 652 Dihedral : 5.137 34.716 530 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer: Outliers : 4.10 % Allowed : 22.65 % Favored : 73.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.22 % 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: -2.67 (0.38), residues: 474 helix: -2.59 (0.50), residues: 92 sheet: -0.66 (0.45), residues: 149 loop : -2.16 (0.39), residues: 233 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 33 HIS 0.002 0.001 HIS A 26 PHE 0.016 0.001 PHE A 177 TYR 0.013 0.001 TYR A 213 ARG 0.002 0.000 ARG D 10 Details of bonding type rmsd hydrogen bonds : bond 0.03034 ( 99) hydrogen bonds : angle 4.98997 ( 240) SS BOND : bond 0.00823 ( 2) SS BOND : angle 1.08648 ( 4) covalent geometry : bond 0.00440 ( 3854) covalent geometry : angle 0.55909 ( 5235) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2013.88 seconds wall clock time: 35 minutes 53.30 seconds (2153.30 seconds total)