Starting phenix.real_space_refine on Wed Feb 12 09:30:33 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6z1o_11031/02_2025/6z1o_11031.cif Found real_map, /net/cci-nas-00/data/ceres_data/6z1o_11031/02_2025/6z1o_11031.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6z1o_11031/02_2025/6z1o_11031.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6z1o_11031/02_2025/6z1o_11031.map" model { file = "/net/cci-nas-00/data/ceres_data/6z1o_11031/02_2025/6z1o_11031.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6z1o_11031/02_2025/6z1o_11031.cif" } resolution = 3.2 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= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 12 5.16 5 C 2436 2.51 5 N 714 2.21 5 O 810 1.98 5 H 3786 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 36 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 7758 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 1293 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 1293 Classifications: {'peptide': 89} Link IDs: {'PTRANS': 2, 'TRANS': 86} Chain breaks: 1 Restraints were copied for chains: C, B, E, D, F Time building chain proxies: 3.48, per 1000 atoms: 0.45 Number of scatterers: 7758 At special positions: 0 Unit cell: (83.2, 82.16, 46.8, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 12 16.00 O 810 8.00 N 714 7.00 C 2436 6.00 H 3786 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 87 " distance=1.99 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: 2.06 Conformation dependent library (CDL) restraints added in 741.2 milliseconds 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 960 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 14 sheets defined 0.0% alpha, 43.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.78 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 10 through 14 Processing sheet with id=AA2, first strand: chain 'A' and resid 17 through 23 Processing sheet with id=AA3, first strand: chain 'A' and resid 25 through 26 Processing sheet with id=AA4, first strand: chain 'A' and resid 28 through 31 Processing sheet with id=AA5, first strand: chain 'A' and resid 34 through 37 Processing sheet with id=AA6, first strand: chain 'A' and resid 43 through 47 Processing sheet with id=AA7, first strand: chain 'A' and resid 60 through 62 Processing sheet with id=AA8, first strand: chain 'A' and resid 64 through 65 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 64 through 65 current: chain 'B' and resid 64 through 65 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 64 through 65 current: chain 'C' and resid 64 through 65 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 64 through 65 current: chain 'D' and resid 64 through 65 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 64 through 65 current: chain 'E' and resid 64 through 65 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 64 through 65 current: chain 'F' and resid 64 through 65 No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'A' and resid 72 through 75 Processing sheet with id=AB1, first strand: chain 'A' and resid 79 through 82 Processing sheet with id=AB2, first strand: chain 'A' and resid 85 through 86 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 85 through 86 current: chain 'B' and resid 85 through 86 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 85 through 86 current: chain 'C' and resid 85 through 86 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 85 through 86 current: chain 'D' and resid 85 through 86 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 85 through 86 current: chain 'E' and resid 85 through 86 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 85 through 86 current: chain 'F' and resid 85 through 86 No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'A' and resid 88 through 91 Processing sheet with id=AB4, first strand: chain 'A' and resid 95 through 97 Processing sheet with id=AB5, first strand: chain 'A' and resid 103 through 106 185 hydrogen bonds defined for protein. 555 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.92 Time building geometry restraints manager: 2.44 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 3786 1.03 - 1.23: 133 1.23 - 1.42: 1637 1.42 - 1.61: 2250 1.61 - 1.81: 12 Bond restraints: 7818 Sorted by residual: bond pdb=" CA ALA D 94 " pdb=" CB ALA D 94 " ideal model delta sigma weight residual 1.530 1.472 0.058 1.24e-02 6.50e+03 2.15e+01 bond pdb=" CA ALA F 94 " pdb=" CB ALA F 94 " ideal model delta sigma weight residual 1.530 1.473 0.057 1.24e-02 6.50e+03 2.13e+01 bond pdb=" CA ALA E 94 " pdb=" CB ALA E 94 " ideal model delta sigma weight residual 1.530 1.473 0.057 1.24e-02 6.50e+03 2.11e+01 bond pdb=" CA ALA C 94 " pdb=" CB ALA C 94 " ideal model delta sigma weight residual 1.530 1.473 0.057 1.24e-02 6.50e+03 2.09e+01 bond pdb=" CA ALA B 94 " pdb=" CB ALA B 94 " ideal model delta sigma weight residual 1.530 1.474 0.056 1.24e-02 6.50e+03 2.06e+01 ... (remaining 7813 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.89: 11065 1.89 - 3.79: 2260 3.79 - 5.68: 459 5.68 - 7.57: 124 7.57 - 9.47: 30 Bond angle restraints: 13938 Sorted by residual: angle pdb=" C PRO B 39 " pdb=" CA PRO B 39 " pdb=" CB PRO B 39 " ideal model delta sigma weight residual 111.11 103.02 8.09 1.17e+00 7.31e-01 4.78e+01 angle pdb=" C PRO F 39 " pdb=" CA PRO F 39 " pdb=" CB PRO F 39 " ideal model delta sigma weight residual 111.11 103.03 8.08 1.17e+00 7.31e-01 4.77e+01 angle pdb=" C PRO A 39 " pdb=" CA PRO A 39 " pdb=" CB PRO A 39 " ideal model delta sigma weight residual 111.11 103.05 8.06 1.17e+00 7.31e-01 4.74e+01 angle pdb=" C PRO C 39 " pdb=" CA PRO C 39 " pdb=" CB PRO C 39 " ideal model delta sigma weight residual 111.11 103.06 8.05 1.17e+00 7.31e-01 4.73e+01 angle pdb=" C PRO E 39 " pdb=" CA PRO E 39 " pdb=" CB PRO E 39 " ideal model delta sigma weight residual 111.11 103.08 8.03 1.17e+00 7.31e-01 4.71e+01 ... (remaining 13933 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.52: 3337 17.52 - 35.04: 295 35.04 - 52.56: 91 52.56 - 70.07: 6 70.07 - 87.59: 6 Dihedral angle restraints: 3735 sinusoidal: 1989 harmonic: 1746 Sorted by residual: dihedral pdb=" C CYS F 87 " pdb=" N CYS F 87 " pdb=" CA CYS F 87 " pdb=" CB CYS F 87 " ideal model delta harmonic sigma weight residual -122.60 -132.10 9.50 0 2.50e+00 1.60e-01 1.44e+01 dihedral pdb=" C CYS C 87 " pdb=" N CYS C 87 " pdb=" CA CYS C 87 " pdb=" CB CYS C 87 " ideal model delta harmonic sigma weight residual -122.60 -132.04 9.44 0 2.50e+00 1.60e-01 1.43e+01 dihedral pdb=" C CYS D 87 " pdb=" N CYS D 87 " pdb=" CA CYS D 87 " pdb=" CB CYS D 87 " ideal model delta harmonic sigma weight residual -122.60 -132.04 9.44 0 2.50e+00 1.60e-01 1.43e+01 ... (remaining 3732 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.072: 222 0.072 - 0.144: 224 0.144 - 0.216: 122 0.216 - 0.289: 26 0.289 - 0.361: 18 Chirality restraints: 612 Sorted by residual: chirality pdb=" CA CYS F 87 " pdb=" N CYS F 87 " pdb=" C CYS F 87 " pdb=" CB CYS F 87 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.25e+00 chirality pdb=" CA CYS A 87 " pdb=" N CYS A 87 " pdb=" C CYS A 87 " pdb=" CB CYS A 87 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.23e+00 chirality pdb=" CA CYS B 87 " pdb=" N CYS B 87 " pdb=" C CYS B 87 " pdb=" CB CYS B 87 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.21e+00 ... (remaining 609 not shown) Planarity restraints: 1224 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN C 95 " 0.222 2.00e-02 2.50e+03 2.76e-01 1.14e+03 pdb=" CG ASN C 95 " -0.013 2.00e-02 2.50e+03 pdb=" OD1 ASN C 95 " -0.223 2.00e-02 2.50e+03 pdb=" ND2 ASN C 95 " 0.010 2.00e-02 2.50e+03 pdb="HD21 ASN C 95 " -0.421 2.00e-02 2.50e+03 pdb="HD22 ASN C 95 " 0.425 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 95 " 0.221 2.00e-02 2.50e+03 2.76e-01 1.14e+03 pdb=" CG ASN A 95 " -0.013 2.00e-02 2.50e+03 pdb=" OD1 ASN A 95 " -0.222 2.00e-02 2.50e+03 pdb=" ND2 ASN A 95 " 0.010 2.00e-02 2.50e+03 pdb="HD21 ASN A 95 " -0.421 2.00e-02 2.50e+03 pdb="HD22 ASN A 95 " 0.425 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN D 95 " 0.221 2.00e-02 2.50e+03 2.76e-01 1.14e+03 pdb=" CG ASN D 95 " -0.013 2.00e-02 2.50e+03 pdb=" OD1 ASN D 95 " -0.222 2.00e-02 2.50e+03 pdb=" ND2 ASN D 95 " 0.010 2.00e-02 2.50e+03 pdb="HD21 ASN D 95 " -0.421 2.00e-02 2.50e+03 pdb="HD22 ASN D 95 " 0.425 2.00e-02 2.50e+03 ... (remaining 1221 not shown) Histogram of nonbonded interaction distances: 1.63 - 2.22: 680 2.22 - 2.82: 16052 2.82 - 3.41: 18609 3.41 - 4.01: 29086 4.01 - 4.60: 40908 Nonbonded interactions: 105335 Sorted by model distance: nonbonded pdb=" OD1 ASN B 68 " pdb=" HG SER B 71 " model vdw 1.628 2.450 nonbonded pdb=" OD1 ASN C 68 " pdb=" HG SER C 71 " model vdw 1.628 2.450 nonbonded pdb=" OD1 ASN D 68 " pdb=" HG SER D 71 " model vdw 1.628 2.450 nonbonded pdb=" OD1 ASN E 68 " pdb=" HG SER E 71 " model vdw 1.629 2.450 nonbonded pdb=" OD1 ASN F 68 " pdb=" HG SER F 71 " model vdw 1.629 2.450 ... (remaining 105330 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: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.320 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: 0.140 Extract box with map and model: 0.270 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 20.340 Find NCS groups from input model: 0.110 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:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7583 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 : 0.013 0.058 4032 Z= 0.871 Angle : 2.231 9.468 5454 Z= 1.581 Chirality : 0.128 0.361 612 Planarity : 0.013 0.047 714 Dihedral : 13.750 52.333 1404 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.24 % Favored : 91.76 % Rotamer: Outliers : 0.00 % Allowed : 11.27 % Favored : 88.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.26 (0.25), residues: 510 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.24 (0.19), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.007 TRP E 34 HIS 0.008 0.005 HIS D 96 PHE 0.018 0.005 PHE A 99 TYR 0.027 0.006 TYR A 86 ARG 0.002 0.001 ARG E 49 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 159 time to evaluate : 0.663 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 80 GLU cc_start: 0.7716 (mt-10) cc_final: 0.7385 (mt-10) REVERT: E 48 PHE cc_start: 0.8219 (m-80) cc_final: 0.7779 (m-80) REVERT: E 104 LYS cc_start: 0.7713 (tttt) cc_final: 0.7414 (ttmt) REVERT: F 84 ASP cc_start: 0.8206 (t0) cc_final: 0.7766 (t0) REVERT: C 48 PHE cc_start: 0.8223 (m-80) cc_final: 0.7935 (m-80) REVERT: C 82 GLU cc_start: 0.8100 (mt-10) cc_final: 0.7602 (mt-10) REVERT: B 48 PHE cc_start: 0.8442 (m-80) cc_final: 0.8135 (m-80) REVERT: A 19 ARG cc_start: 0.7976 (ttt180) cc_final: 0.7148 (mmp-170) REVERT: A 34 TRP cc_start: 0.7391 (t-100) cc_final: 0.6958 (t60) REVERT: A 80 GLU cc_start: 0.6973 (mt-10) cc_final: 0.6766 (mt-10) REVERT: A 104 LYS cc_start: 0.7866 (tttt) cc_final: 0.7452 (tttt) outliers start: 0 outliers final: 0 residues processed: 159 average time/residue: 0.4336 time to fit residues: 81.2254 Evaluate side-chains 99 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 99 time to evaluate : 0.624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 40 optimal weight: 0.9990 chunk 36 optimal weight: 0.5980 chunk 20 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 24 optimal weight: 0.9980 chunk 19 optimal weight: 0.9990 chunk 37 optimal weight: 0.2980 chunk 14 optimal weight: 0.8980 chunk 22 optimal weight: 0.3980 chunk 28 optimal weight: 1.9990 chunk 43 optimal weight: 0.2980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 37 GLN D 68 ASN C 68 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.129689 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.121420 restraints weight = 20239.701| |-----------------------------------------------------------------------------| r_work (start): 0.3929 rms_B_bonded: 2.23 r_work: 0.3851 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3751 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3751 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7823 moved from start: 0.4269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 4032 Z= 0.210 Angle : 0.648 4.381 5454 Z= 0.362 Chirality : 0.047 0.136 612 Planarity : 0.005 0.042 714 Dihedral : 6.434 19.707 576 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 1.88 % Allowed : 15.96 % Favored : 82.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.69 (0.27), residues: 510 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.80 (0.21), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 34 HIS 0.002 0.001 HIS F 96 PHE 0.008 0.001 PHE F 99 TYR 0.020 0.003 TYR E 86 ARG 0.002 0.000 ARG A 60 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 99 time to evaluate : 0.646 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 46 VAL cc_start: 0.9197 (m) cc_final: 0.8945 (t) REVERT: C 49 ARG cc_start: 0.6321 (tpt90) cc_final: 0.5903 (tpt90) REVERT: B 48 PHE cc_start: 0.8585 (m-80) cc_final: 0.8353 (m-80) REVERT: B 97 GLN cc_start: 0.8975 (mp10) cc_final: 0.8627 (mt0) REVERT: A 19 ARG cc_start: 0.8402 (ttt180) cc_final: 0.7320 (mmp-170) REVERT: A 23 GLN cc_start: 0.7801 (tt0) cc_final: 0.7575 (tt0) REVERT: A 34 TRP cc_start: 0.8107 (t-100) cc_final: 0.6960 (t60) REVERT: A 104 LYS cc_start: 0.7707 (tttt) cc_final: 0.7185 (tttm) outliers start: 8 outliers final: 5 residues processed: 104 average time/residue: 0.3184 time to fit residues: 41.4042 Evaluate side-chains 84 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 79 time to evaluate : 0.712 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 71 SER Chi-restraints excluded: chain F residue 81 ASP Chi-restraints excluded: chain A residue 71 SER Chi-restraints excluded: chain A residue 89 SER Chi-restraints excluded: chain A residue 93 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 38 optimal weight: 1.9990 chunk 41 optimal weight: 0.9990 chunk 8 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 37 optimal weight: 0.6980 chunk 31 optimal weight: 0.9990 chunk 19 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 overall best weight: 1.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 88 ASN A 36 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.113288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.106219 restraints weight = 21528.482| |-----------------------------------------------------------------------------| r_work (start): 0.3711 rms_B_bonded: 2.07 r_work: 0.3637 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3546 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3546 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 0.5801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 4032 Z= 0.367 Angle : 0.695 4.882 5454 Z= 0.388 Chirality : 0.047 0.133 612 Planarity : 0.005 0.037 714 Dihedral : 6.360 17.086 576 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 3.29 % Allowed : 16.43 % Favored : 80.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.69 (0.27), residues: 510 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.80 (0.21), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP E 34 HIS 0.002 0.001 HIS F 96 PHE 0.011 0.001 PHE F 99 TYR 0.024 0.003 TYR F 85 ARG 0.003 0.001 ARG A 90 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 78 time to evaluate : 0.633 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 48 PHE cc_start: 0.8375 (OUTLIER) cc_final: 0.8143 (t80) REVERT: F 80 GLU cc_start: 0.8220 (mt-10) cc_final: 0.8009 (mt-10) REVERT: C 48 PHE cc_start: 0.8365 (OUTLIER) cc_final: 0.7934 (t80) REVERT: C 80 GLU cc_start: 0.8368 (mt-10) cc_final: 0.8128 (mt-10) REVERT: B 48 PHE cc_start: 0.8700 (m-80) cc_final: 0.8493 (m-80) REVERT: B 84 ASP cc_start: 0.8842 (OUTLIER) cc_final: 0.8175 (t0) REVERT: B 97 GLN cc_start: 0.9111 (mp10) cc_final: 0.8809 (mt0) REVERT: A 90 ARG cc_start: 0.8614 (ttp80) cc_final: 0.6829 (tpm170) outliers start: 14 outliers final: 9 residues processed: 84 average time/residue: 0.3681 time to fit residues: 37.7379 Evaluate side-chains 77 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 65 time to evaluate : 0.684 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 48 PHE Chi-restraints excluded: chain D residue 71 SER Chi-restraints excluded: chain E residue 48 PHE Chi-restraints excluded: chain E residue 105 LEU Chi-restraints excluded: chain F residue 48 PHE Chi-restraints excluded: chain F residue 71 SER Chi-restraints excluded: chain F residue 81 ASP Chi-restraints excluded: chain C residue 48 PHE Chi-restraints excluded: chain B residue 84 ASP Chi-restraints excluded: chain B residue 93 SER Chi-restraints excluded: chain A residue 71 SER Chi-restraints excluded: chain A residue 93 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 22 optimal weight: 1.9990 chunk 30 optimal weight: 0.5980 chunk 20 optimal weight: 2.9990 chunk 33 optimal weight: 0.6980 chunk 9 optimal weight: 1.9990 chunk 5 optimal weight: 0.8980 chunk 40 optimal weight: 0.0770 chunk 1 optimal weight: 0.5980 chunk 16 optimal weight: 0.9980 chunk 44 optimal weight: 1.9990 chunk 27 optimal weight: 0.5980 overall best weight: 0.5138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.116086 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.108692 restraints weight = 21429.523| |-----------------------------------------------------------------------------| r_work (start): 0.3758 rms_B_bonded: 2.16 r_work: 0.3688 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3593 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3593 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.6214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4032 Z= 0.188 Angle : 0.579 4.396 5454 Z= 0.320 Chirality : 0.044 0.132 612 Planarity : 0.004 0.034 714 Dihedral : 5.987 16.397 576 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 3.52 % Allowed : 18.31 % Favored : 78.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.59 (0.27), residues: 510 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.73 (0.21), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 34 HIS 0.002 0.001 HIS B 96 PHE 0.004 0.001 PHE A 48 TYR 0.015 0.001 TYR F 86 ARG 0.002 0.000 ARG D 90 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 73 time to evaluate : 0.675 Fit side-chains revert: symmetry clash REVERT: D 48 PHE cc_start: 0.8314 (OUTLIER) cc_final: 0.8094 (t80) REVERT: E 80 GLU cc_start: 0.8589 (OUTLIER) cc_final: 0.8048 (mm-30) REVERT: E 104 LYS cc_start: 0.7814 (tttt) cc_final: 0.7180 (tmtt) REVERT: F 80 GLU cc_start: 0.8301 (mt-10) cc_final: 0.8088 (mt-10) REVERT: C 48 PHE cc_start: 0.8249 (OUTLIER) cc_final: 0.7793 (t80) REVERT: B 97 GLN cc_start: 0.9106 (mp10) cc_final: 0.8858 (mt0) REVERT: A 90 ARG cc_start: 0.8491 (ttp80) cc_final: 0.6802 (tpm170) outliers start: 15 outliers final: 9 residues processed: 77 average time/residue: 0.3650 time to fit residues: 34.5020 Evaluate side-chains 74 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 62 time to evaluate : 0.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 48 PHE Chi-restraints excluded: chain D residue 71 SER Chi-restraints excluded: chain D residue 84 ASP Chi-restraints excluded: chain E residue 48 PHE Chi-restraints excluded: chain E residue 80 GLU Chi-restraints excluded: chain E residue 105 LEU Chi-restraints excluded: chain F residue 48 PHE Chi-restraints excluded: chain F residue 71 SER Chi-restraints excluded: chain F residue 81 ASP Chi-restraints excluded: chain C residue 48 PHE Chi-restraints excluded: chain A residue 71 SER Chi-restraints excluded: chain A residue 93 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 9 optimal weight: 0.9980 chunk 35 optimal weight: 0.8980 chunk 5 optimal weight: 0.9980 chunk 2 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 chunk 29 optimal weight: 0.9980 chunk 3 optimal weight: 0.7980 chunk 30 optimal weight: 0.9980 chunk 40 optimal weight: 1.9990 chunk 0 optimal weight: 0.9990 chunk 46 optimal weight: 0.5980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 88 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.112756 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.105516 restraints weight = 21673.232| |-----------------------------------------------------------------------------| r_work (start): 0.3725 rms_B_bonded: 2.17 r_work: 0.3659 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3564 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3564 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.6533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 4032 Z= 0.280 Angle : 0.608 4.666 5454 Z= 0.336 Chirality : 0.045 0.128 612 Planarity : 0.004 0.033 714 Dihedral : 5.976 16.473 576 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 4.46 % Allowed : 16.67 % Favored : 78.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.62 (0.27), residues: 510 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.75 (0.21), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 34 HIS 0.003 0.001 HIS F 96 PHE 0.006 0.001 PHE F 99 TYR 0.016 0.002 TYR F 85 ARG 0.003 0.000 ARG D 49 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 67 time to evaluate : 0.614 Fit side-chains REVERT: D 48 PHE cc_start: 0.8318 (OUTLIER) cc_final: 0.8097 (t80) REVERT: E 80 GLU cc_start: 0.8577 (OUTLIER) cc_final: 0.7978 (mm-30) REVERT: E 104 LYS cc_start: 0.7921 (tttt) cc_final: 0.7291 (tmtt) REVERT: C 48 PHE cc_start: 0.8252 (OUTLIER) cc_final: 0.7819 (t80) REVERT: B 97 GLN cc_start: 0.9156 (mp10) cc_final: 0.8851 (mt0) REVERT: A 90 ARG cc_start: 0.8590 (ttp80) cc_final: 0.6856 (tpm170) outliers start: 19 outliers final: 13 residues processed: 74 average time/residue: 0.2968 time to fit residues: 28.2467 Evaluate side-chains 81 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 65 time to evaluate : 0.637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 48 PHE Chi-restraints excluded: chain D residue 71 SER Chi-restraints excluded: chain D residue 81 ASP Chi-restraints excluded: chain D residue 84 ASP Chi-restraints excluded: chain E residue 48 PHE Chi-restraints excluded: chain E residue 80 GLU Chi-restraints excluded: chain E residue 105 LEU Chi-restraints excluded: chain F residue 48 PHE Chi-restraints excluded: chain F residue 71 SER Chi-restraints excluded: chain F residue 81 ASP Chi-restraints excluded: chain C residue 48 PHE Chi-restraints excluded: chain B residue 93 SER Chi-restraints excluded: chain A residue 34 TRP Chi-restraints excluded: chain A residue 71 SER Chi-restraints excluded: chain A residue 88 ASN Chi-restraints excluded: chain A residue 93 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 36 optimal weight: 3.9990 chunk 45 optimal weight: 0.0050 chunk 42 optimal weight: 1.9990 chunk 23 optimal weight: 0.4980 chunk 7 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 25 optimal weight: 0.9990 chunk 46 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 16 optimal weight: 0.9990 chunk 47 optimal weight: 0.9980 overall best weight: 0.6998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 88 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.113357 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.106142 restraints weight = 21615.468| |-----------------------------------------------------------------------------| r_work (start): 0.3733 rms_B_bonded: 2.18 r_work: 0.3662 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3564 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3564 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 0.6644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 4032 Z= 0.231 Angle : 0.584 4.542 5454 Z= 0.323 Chirality : 0.044 0.129 612 Planarity : 0.004 0.033 714 Dihedral : 5.898 16.376 576 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 4.93 % Allowed : 16.20 % Favored : 78.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.62 (0.27), residues: 510 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.75 (0.21), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 34 HIS 0.003 0.001 HIS F 96 PHE 0.003 0.001 PHE A 61 TYR 0.013 0.002 TYR F 85 ARG 0.003 0.000 ARG D 49 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 66 time to evaluate : 0.654 Fit side-chains REVERT: D 48 PHE cc_start: 0.8306 (OUTLIER) cc_final: 0.8059 (t80) REVERT: E 80 GLU cc_start: 0.8564 (OUTLIER) cc_final: 0.7992 (mm-30) REVERT: E 104 LYS cc_start: 0.7838 (tttt) cc_final: 0.7136 (tmtt) REVERT: C 48 PHE cc_start: 0.8254 (OUTLIER) cc_final: 0.7837 (t80) REVERT: A 90 ARG cc_start: 0.8575 (ttp80) cc_final: 0.6881 (tpm170) outliers start: 21 outliers final: 14 residues processed: 73 average time/residue: 0.3279 time to fit residues: 29.8528 Evaluate side-chains 80 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 63 time to evaluate : 0.650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 34 TRP Chi-restraints excluded: chain D residue 48 PHE Chi-restraints excluded: chain D residue 71 SER Chi-restraints excluded: chain D residue 81 ASP Chi-restraints excluded: chain D residue 84 ASP Chi-restraints excluded: chain E residue 48 PHE Chi-restraints excluded: chain E residue 80 GLU Chi-restraints excluded: chain E residue 105 LEU Chi-restraints excluded: chain F residue 48 PHE Chi-restraints excluded: chain F residue 71 SER Chi-restraints excluded: chain F residue 81 ASP Chi-restraints excluded: chain C residue 48 PHE Chi-restraints excluded: chain A residue 34 TRP Chi-restraints excluded: chain A residue 71 SER Chi-restraints excluded: chain A residue 84 ASP Chi-restraints excluded: chain A residue 89 SER Chi-restraints excluded: chain A residue 93 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 33 optimal weight: 0.9980 chunk 43 optimal weight: 0.6980 chunk 26 optimal weight: 1.9990 chunk 3 optimal weight: 0.9980 chunk 35 optimal weight: 0.3980 chunk 9 optimal weight: 0.9980 chunk 28 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 chunk 17 optimal weight: 0.5980 chunk 12 optimal weight: 2.9990 chunk 11 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.115131 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.107811 restraints weight = 21638.757| |-----------------------------------------------------------------------------| r_work (start): 0.3766 rms_B_bonded: 2.23 r_work: 0.3695 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3600 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3600 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 moved from start: 0.6800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 4032 Z= 0.226 Angle : 0.573 4.538 5454 Z= 0.317 Chirality : 0.044 0.128 612 Planarity : 0.003 0.032 714 Dihedral : 5.814 19.670 576 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 4.23 % Allowed : 17.14 % Favored : 78.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.58 (0.28), residues: 510 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.72 (0.21), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 34 HIS 0.003 0.001 HIS F 96 PHE 0.004 0.001 PHE F 99 TYR 0.012 0.001 TYR F 85 ARG 0.002 0.000 ARG D 49 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 67 time to evaluate : 0.612 Fit side-chains REVERT: D 48 PHE cc_start: 0.8303 (OUTLIER) cc_final: 0.8061 (t80) REVERT: E 80 GLU cc_start: 0.8704 (OUTLIER) cc_final: 0.8139 (mm-30) REVERT: E 104 LYS cc_start: 0.7884 (tttt) cc_final: 0.7156 (tmtt) REVERT: C 48 PHE cc_start: 0.8270 (OUTLIER) cc_final: 0.7844 (t80) REVERT: B 90 ARG cc_start: 0.8533 (ttp80) cc_final: 0.8332 (ttt180) REVERT: A 90 ARG cc_start: 0.8550 (ttp80) cc_final: 0.6860 (tpm170) outliers start: 18 outliers final: 13 residues processed: 72 average time/residue: 0.3820 time to fit residues: 33.5434 Evaluate side-chains 79 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 63 time to evaluate : 0.663 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 34 TRP Chi-restraints excluded: chain D residue 48 PHE Chi-restraints excluded: chain D residue 71 SER Chi-restraints excluded: chain D residue 81 ASP Chi-restraints excluded: chain D residue 84 ASP Chi-restraints excluded: chain E residue 48 PHE Chi-restraints excluded: chain E residue 80 GLU Chi-restraints excluded: chain E residue 105 LEU Chi-restraints excluded: chain F residue 48 PHE Chi-restraints excluded: chain F residue 71 SER Chi-restraints excluded: chain F residue 81 ASP Chi-restraints excluded: chain C residue 48 PHE Chi-restraints excluded: chain A residue 34 TRP Chi-restraints excluded: chain A residue 71 SER Chi-restraints excluded: chain A residue 89 SER Chi-restraints excluded: chain A residue 93 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 22 optimal weight: 1.9990 chunk 35 optimal weight: 0.1980 chunk 36 optimal weight: 2.9990 chunk 16 optimal weight: 0.9980 chunk 3 optimal weight: 0.9990 chunk 43 optimal weight: 0.3980 chunk 0 optimal weight: 1.9990 chunk 11 optimal weight: 0.5980 chunk 12 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 39 optimal weight: 2.9990 overall best weight: 0.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 23 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.115408 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.108186 restraints weight = 21732.153| |-----------------------------------------------------------------------------| r_work (start): 0.3767 rms_B_bonded: 2.21 r_work: 0.3704 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3609 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.3609 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8019 moved from start: 0.6928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4032 Z= 0.218 Angle : 0.571 4.522 5454 Z= 0.314 Chirality : 0.044 0.126 612 Planarity : 0.003 0.031 714 Dihedral : 5.753 18.860 576 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 4.46 % Allowed : 17.14 % Favored : 78.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.53 (0.28), residues: 510 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.68 (0.21), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 34 HIS 0.003 0.001 HIS F 96 PHE 0.004 0.001 PHE E 48 TYR 0.012 0.001 TYR F 85 ARG 0.002 0.000 ARG D 49 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 67 time to evaluate : 0.623 Fit side-chains REVERT: D 48 PHE cc_start: 0.8296 (OUTLIER) cc_final: 0.8074 (t80) REVERT: E 80 GLU cc_start: 0.8718 (OUTLIER) cc_final: 0.8301 (mm-30) REVERT: E 104 LYS cc_start: 0.7981 (tttt) cc_final: 0.7341 (tmtt) REVERT: C 48 PHE cc_start: 0.8292 (OUTLIER) cc_final: 0.7846 (t80) REVERT: B 85 TYR cc_start: 0.8468 (t80) cc_final: 0.8223 (t80) REVERT: B 90 ARG cc_start: 0.8571 (ttp80) cc_final: 0.8360 (ttt180) REVERT: A 90 ARG cc_start: 0.8569 (ttp80) cc_final: 0.7010 (tpm170) outliers start: 19 outliers final: 13 residues processed: 74 average time/residue: 0.3744 time to fit residues: 34.3314 Evaluate side-chains 81 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 65 time to evaluate : 0.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 48 PHE Chi-restraints excluded: chain D residue 71 SER Chi-restraints excluded: chain D residue 81 ASP Chi-restraints excluded: chain D residue 84 ASP Chi-restraints excluded: chain E residue 48 PHE Chi-restraints excluded: chain E residue 80 GLU Chi-restraints excluded: chain E residue 105 LEU Chi-restraints excluded: chain F residue 48 PHE Chi-restraints excluded: chain F residue 71 SER Chi-restraints excluded: chain C residue 48 PHE Chi-restraints excluded: chain B residue 93 SER Chi-restraints excluded: chain A residue 34 TRP Chi-restraints excluded: chain A residue 48 PHE Chi-restraints excluded: chain A residue 71 SER Chi-restraints excluded: chain A residue 89 SER Chi-restraints excluded: chain A residue 93 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 9 optimal weight: 0.9990 chunk 15 optimal weight: 2.9990 chunk 5 optimal weight: 0.3980 chunk 21 optimal weight: 0.9990 chunk 35 optimal weight: 0.4980 chunk 45 optimal weight: 0.9990 chunk 47 optimal weight: 1.9990 chunk 0 optimal weight: 0.9990 chunk 26 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 chunk 28 optimal weight: 3.9990 overall best weight: 0.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.114257 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.107064 restraints weight = 21976.329| |-----------------------------------------------------------------------------| r_work (start): 0.3760 rms_B_bonded: 2.21 r_work: 0.3696 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3600 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3600 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.6992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 4032 Z= 0.248 Angle : 0.584 4.604 5454 Z= 0.321 Chirality : 0.044 0.125 612 Planarity : 0.003 0.032 714 Dihedral : 5.791 18.559 576 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 3.99 % Allowed : 17.61 % Favored : 78.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.50 (0.28), residues: 510 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.66 (0.21), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 34 HIS 0.002 0.001 HIS F 96 PHE 0.003 0.001 PHE F 99 TYR 0.013 0.002 TYR F 85 ARG 0.002 0.000 ARG D 49 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 70 time to evaluate : 0.611 Fit side-chains REVERT: D 48 PHE cc_start: 0.8321 (OUTLIER) cc_final: 0.8071 (t80) REVERT: E 80 GLU cc_start: 0.8753 (mm-30) cc_final: 0.8223 (mm-30) REVERT: E 104 LYS cc_start: 0.7955 (tttt) cc_final: 0.7186 (tmtt) REVERT: F 80 GLU cc_start: 0.8348 (mt-10) cc_final: 0.8061 (mt-10) REVERT: C 48 PHE cc_start: 0.8276 (OUTLIER) cc_final: 0.7864 (t80) REVERT: A 90 ARG cc_start: 0.8544 (ttp80) cc_final: 0.7009 (tpm170) outliers start: 17 outliers final: 14 residues processed: 76 average time/residue: 0.3432 time to fit residues: 32.4161 Evaluate side-chains 84 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 68 time to evaluate : 0.632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 48 PHE Chi-restraints excluded: chain D residue 71 SER Chi-restraints excluded: chain D residue 81 ASP Chi-restraints excluded: chain D residue 84 ASP Chi-restraints excluded: chain E residue 48 PHE Chi-restraints excluded: chain E residue 105 LEU Chi-restraints excluded: chain F residue 48 PHE Chi-restraints excluded: chain F residue 71 SER Chi-restraints excluded: chain F residue 81 ASP Chi-restraints excluded: chain C residue 48 PHE Chi-restraints excluded: chain B residue 93 SER Chi-restraints excluded: chain A residue 34 TRP Chi-restraints excluded: chain A residue 48 PHE Chi-restraints excluded: chain A residue 71 SER Chi-restraints excluded: chain A residue 89 SER Chi-restraints excluded: chain A residue 93 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 1 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 28 optimal weight: 0.9980 chunk 35 optimal weight: 0.9990 chunk 14 optimal weight: 0.8980 chunk 5 optimal weight: 0.0970 chunk 25 optimal weight: 0.5980 chunk 41 optimal weight: 0.9980 chunk 43 optimal weight: 0.5980 chunk 31 optimal weight: 1.9990 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.114084 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.107184 restraints weight = 21909.872| |-----------------------------------------------------------------------------| r_work (start): 0.3767 rms_B_bonded: 2.17 r_work: 0.3703 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3610 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3610 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 moved from start: 0.7096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 4032 Z= 0.218 Angle : 0.587 5.449 5454 Z= 0.318 Chirality : 0.044 0.124 612 Planarity : 0.003 0.031 714 Dihedral : 5.743 18.472 576 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 3.52 % Allowed : 18.31 % Favored : 78.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.45 (0.28), residues: 510 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.62 (0.21), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 34 HIS 0.003 0.001 HIS F 96 PHE 0.005 0.001 PHE A 48 TYR 0.012 0.001 TYR F 85 ARG 0.002 0.000 ARG A 49 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 71 time to evaluate : 0.634 Fit side-chains REVERT: D 48 PHE cc_start: 0.8261 (OUTLIER) cc_final: 0.8058 (t80) REVERT: E 80 GLU cc_start: 0.8755 (mm-30) cc_final: 0.8121 (mm-30) REVERT: E 104 LYS cc_start: 0.7940 (tttt) cc_final: 0.7265 (tmtt) REVERT: F 80 GLU cc_start: 0.8301 (mt-10) cc_final: 0.7999 (mt-10) REVERT: C 48 PHE cc_start: 0.8293 (OUTLIER) cc_final: 0.7830 (t80) REVERT: B 85 TYR cc_start: 0.8374 (t80) cc_final: 0.8147 (t80) REVERT: A 90 ARG cc_start: 0.8424 (ttp80) cc_final: 0.6917 (tpm170) outliers start: 15 outliers final: 13 residues processed: 76 average time/residue: 0.3471 time to fit residues: 32.8513 Evaluate side-chains 82 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 67 time to evaluate : 0.667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 48 PHE Chi-restraints excluded: chain D residue 71 SER Chi-restraints excluded: chain D residue 81 ASP Chi-restraints excluded: chain D residue 84 ASP Chi-restraints excluded: chain E residue 48 PHE Chi-restraints excluded: chain E residue 105 LEU Chi-restraints excluded: chain F residue 48 PHE Chi-restraints excluded: chain F residue 71 SER Chi-restraints excluded: chain F residue 81 ASP Chi-restraints excluded: chain C residue 48 PHE Chi-restraints excluded: chain B residue 93 SER Chi-restraints excluded: chain A residue 34 TRP Chi-restraints excluded: chain A residue 71 SER Chi-restraints excluded: chain A residue 89 SER Chi-restraints excluded: chain A residue 93 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 41 optimal weight: 0.9990 chunk 47 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 43 optimal weight: 0.6980 chunk 28 optimal weight: 2.9990 chunk 1 optimal weight: 0.9990 chunk 10 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 21 optimal weight: 0.1980 overall best weight: 0.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.112576 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.105756 restraints weight = 21522.141| |-----------------------------------------------------------------------------| r_work (start): 0.3739 rms_B_bonded: 2.10 r_work: 0.3675 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3583 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.3583 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.7175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.030 4032 Z= 0.306 Angle : 0.623 5.921 5454 Z= 0.339 Chirality : 0.045 0.124 612 Planarity : 0.003 0.031 714 Dihedral : 5.886 17.902 576 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 3.99 % Allowed : 18.08 % Favored : 77.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.46 (0.28), residues: 510 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.63 (0.21), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 34 HIS 0.002 0.001 HIS F 96 PHE 0.003 0.001 PHE F 99 TYR 0.016 0.002 TYR B 85 ARG 0.002 0.000 ARG C 28 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4429.62 seconds wall clock time: 78 minutes 51.76 seconds (4731.76 seconds total)