Starting phenix.real_space_refine on Wed Mar 12 09:33:20 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6z1o_11031/03_2025/6z1o_11031.cif Found real_map, /net/cci-nas-00/data/ceres_data/6z1o_11031/03_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_11031/03_2025/6z1o_11031.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6z1o_11031/03_2025/6z1o_11031.map" model { file = "/net/cci-nas-00/data/ceres_data/6z1o_11031/03_2025/6z1o_11031.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6z1o_11031/03_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-5624/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: 3.51, 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: 2.04 Conformation dependent library (CDL) restraints added in 690.2 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: 1.07 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: 2.85 Time building geometry restraints manager: 2.47 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: 1.840 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: 0.310 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 21.220 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.020 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:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.540 ------------------------------------------------------------------------------- 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 : 0.647 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: 0.4229 time to fit residues: 79.2060 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 : 0.656 ------------------------------------------------------------------------------- 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: 0.5980 chunk 28 optimal weight: 1.9990 chunk 43 optimal weight: 0.2980 overall best weight: 0.5380 ------------------------------------------------------------------------------- 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 A 36 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.128906 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 23)----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.120778 restraints weight = 20353.060| |-----------------------------------------------------------------------------| r_work (start): 0.3921 rms_B_bonded: 2.19 r_work: 0.3849 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3752 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3752 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7821 moved from start: 0.4235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 4032 Z= 0.213 Angle : 0.654 4.419 5454 Z= 0.366 Chirality : 0.047 0.136 612 Planarity : 0.005 0.043 714 Dihedral : 6.408 19.492 576 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 1.88 % Allowed : 16.20 % Favored : 81.92 % 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: -3.68 (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 0.010 0.001 TRP C 34 HIS 0.002 0.001 HIS F 96 PHE 0.009 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 106 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 98 time to evaluate : 0.786 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 48 PHE cc_start: 0.8402 (m-80) cc_final: 0.8200 (t80) REVERT: E 104 LYS cc_start: 0.7775 (tttt) cc_final: 0.7158 (tmtt) REVERT: C 46 VAL cc_start: 0.9166 (m) cc_final: 0.8914 (t) REVERT: C 49 ARG cc_start: 0.6405 (tpt90) cc_final: 0.5951 (tpt90) REVERT: B 48 PHE cc_start: 0.8587 (m-80) cc_final: 0.8303 (m-80) REVERT: B 97 GLN cc_start: 0.8980 (mp10) cc_final: 0.8622 (mt0) REVERT: A 19 ARG cc_start: 0.8393 (ttt180) cc_final: 0.7319 (mmp-170) REVERT: A 23 GLN cc_start: 0.7833 (tt0) cc_final: 0.7594 (tt0) REVERT: A 34 TRP cc_start: 0.8113 (t-100) cc_final: 0.6994 (t60) REVERT: A 104 LYS cc_start: 0.7724 (tttt) cc_final: 0.7208 (tttm) outliers start: 8 outliers final: 5 residues processed: 102 average time/residue: 0.3288 time to fit residues: 42.7449 Evaluate side-chains 81 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 76 time to evaluate : 0.617 ------------------------------------------------------------------------------- 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: 2.9990 chunk 41 optimal weight: 0.9980 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: 0.1980 chunk 31 optimal weight: 0.8980 chunk 19 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.114268 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.106694 restraints weight = 21313.996| |-----------------------------------------------------------------------------| r_work (start): 0.3729 rms_B_bonded: 2.12 r_work: 0.3655 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3558 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.3558 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 moved from start: 0.5630 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= 0.323 Angle : 0.672 4.806 5454 Z= 0.374 Chirality : 0.046 0.130 612 Planarity : 0.005 0.037 714 Dihedral : 6.225 16.976 576 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 3.29 % Allowed : 16.20 % Favored : 80.52 % 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: -3.73 (0.27), residues: 510 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.83 (0.21), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP E 34 HIS 0.002 0.001 HIS F 96 PHE 0.010 0.001 PHE F 99 TYR 0.021 0.002 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 94 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 80 time to evaluate : 0.623 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 48 PHE cc_start: 0.8324 (OUTLIER) cc_final: 0.8109 (t80) REVERT: E 80 GLU cc_start: 0.8449 (OUTLIER) cc_final: 0.8002 (mm-30) REVERT: C 48 PHE cc_start: 0.8368 (OUTLIER) cc_final: 0.7944 (t80) REVERT: B 48 PHE cc_start: 0.8682 (m-80) cc_final: 0.8443 (m-80) REVERT: B 97 GLN cc_start: 0.9109 (mp10) cc_final: 0.8816 (mt0) REVERT: A 80 GLU cc_start: 0.8313 (mt-10) cc_final: 0.8041 (mt-10) REVERT: A 90 ARG cc_start: 0.8525 (ttp80) cc_final: 0.6789 (tpm170) REVERT: A 104 LYS cc_start: 0.7792 (tttt) cc_final: 0.7570 (tptt) outliers start: 14 outliers final: 8 residues processed: 86 average time/residue: 0.3588 time to fit residues: 37.9063 Evaluate side-chains 78 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 67 time to evaluate : 0.669 ------------------------------------------------------------------------------- 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 80 GLU Chi-restraints excluded: chain E residue 81 ASP 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 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: 1.9990 chunk 20 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 5 optimal weight: 0.9980 chunk 40 optimal weight: 0.9990 chunk 1 optimal weight: 0.6980 chunk 16 optimal weight: 0.9990 chunk 44 optimal weight: 1.9990 chunk 27 optimal weight: 0.6980 overall best weight: 0.8784 ------------------------------------------------------------------------------- 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 = 0.3821 r_free = 0.3821 target = 0.113991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.106826 restraints weight = 21712.833| |-----------------------------------------------------------------------------| r_work (start): 0.3728 rms_B_bonded: 2.16 r_work: 0.3655 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3561 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3561 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.6234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 4032 Z= 0.275 Angle : 0.611 4.627 5454 Z= 0.339 Chirality : 0.045 0.136 612 Planarity : 0.004 0.035 714 Dihedral : 6.092 19.111 576 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 3.76 % Allowed : 16.90 % Favored : 79.34 % 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: -3.65 (0.27), residues: 510 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.77 (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 0.004 0.001 PHE A 48 TYR 0.014 0.002 TYR F 86 ARG 0.003 0.000 ARG D 49 *********************** 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 86 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 70 time to evaluate : 0.642 Fit side-chains revert: symmetry clash REVERT: D 48 PHE cc_start: 0.8361 (OUTLIER) cc_final: 0.8088 (t80) REVERT: D 80 GLU cc_start: 0.8267 (mt-10) cc_final: 0.8056 (mt-10) REVERT: E 80 GLU cc_start: 0.8540 (mt-10) cc_final: 0.8144 (mm-30) REVERT: E 104 LYS cc_start: 0.7841 (tttt) cc_final: 0.7195 (tmtt) REVERT: C 48 PHE cc_start: 0.8243 (OUTLIER) cc_final: 0.7794 (t80) REVERT: B 48 PHE cc_start: 0.8673 (m-80) cc_final: 0.8473 (m-80) REVERT: B 84 ASP cc_start: 0.8660 (OUTLIER) cc_final: 0.8182 (t0) REVERT: B 97 GLN cc_start: 0.9125 (mp10) cc_final: 0.8851 (mt0) REVERT: A 25 ASP cc_start: 0.7801 (p0) cc_final: 0.7599 (p0) REVERT: A 90 ARG cc_start: 0.8511 (ttp80) cc_final: 0.6827 (tpm170) outliers start: 16 outliers final: 8 residues processed: 76 average time/residue: 0.3451 time to fit residues: 32.5435 Evaluate side-chains 75 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 64 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 84 ASP Chi-restraints excluded: chain E residue 81 ASP 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 84 ASP 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: 0.9990 chunk 35 optimal weight: 0.7980 chunk 5 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 29 optimal weight: 0.5980 chunk 3 optimal weight: 0.9980 chunk 30 optimal weight: 0.9990 chunk 40 optimal weight: 1.9990 chunk 0 optimal weight: 0.9990 chunk 46 optimal weight: 0.5980 overall best weight: 0.7982 ------------------------------------------------------------------------------- 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 = 0.3820 r_free = 0.3820 target = 0.113532 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.106281 restraints weight = 21630.391| |-----------------------------------------------------------------------------| r_work (start): 0.3723 rms_B_bonded: 2.17 r_work: 0.3656 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3560 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3560 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 moved from start: 0.6565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 4032 Z= 0.258 Angle : 0.594 4.609 5454 Z= 0.329 Chirality : 0.044 0.128 612 Planarity : 0.004 0.034 714 Dihedral : 5.938 18.603 576 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 3.99 % Allowed : 16.20 % Favored : 79.81 % 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 0.004 0.001 PHE F 99 TYR 0.014 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 85 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 68 time to evaluate : 0.635 Fit side-chains REVERT: D 48 PHE cc_start: 0.8324 (OUTLIER) cc_final: 0.8061 (t80) REVERT: D 80 GLU cc_start: 0.8357 (mt-10) cc_final: 0.8041 (mt-10) REVERT: E 80 GLU cc_start: 0.8505 (mt-10) cc_final: 0.7954 (mm-30) REVERT: E 104 LYS cc_start: 0.7851 (tttt) cc_final: 0.7217 (tmtt) REVERT: C 48 PHE cc_start: 0.8252 (OUTLIER) cc_final: 0.7823 (t80) REVERT: B 84 ASP cc_start: 0.8433 (t0) cc_final: 0.8160 (t0) REVERT: B 97 GLN cc_start: 0.9134 (mp10) cc_final: 0.8830 (mt0) REVERT: A 90 ARG cc_start: 0.8587 (ttp80) cc_final: 0.6905 (tpm170) outliers start: 17 outliers final: 15 residues processed: 75 average time/residue: 0.3095 time to fit residues: 29.5191 Evaluate side-chains 82 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 65 time to evaluate : 0.617 ------------------------------------------------------------------------------- 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 81 ASP Chi-restraints excluded: chain E residue 93 SER 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 36 optimal weight: 3.9990 chunk 45 optimal weight: 0.6980 chunk 42 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 chunk 29 optimal weight: 0.9980 chunk 25 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 16 optimal weight: 0.8980 chunk 47 optimal weight: 0.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- 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 = 0.3788 r_free = 0.3788 target = 0.111004 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.103980 restraints weight = 21954.464| |-----------------------------------------------------------------------------| r_work (start): 0.3696 rms_B_bonded: 2.14 r_work: 0.3629 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3536 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3536 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 moved from start: 0.6780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.029 4032 Z= 0.345 Angle : 0.631 4.748 5454 Z= 0.351 Chirality : 0.045 0.130 612 Planarity : 0.004 0.033 714 Dihedral : 6.079 19.128 576 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 4.93 % Allowed : 15.73 % Favored : 79.34 % 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: -3.61 (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 0.009 0.001 TRP E 34 HIS 0.003 0.001 HIS F 96 PHE 0.004 0.001 PHE F 99 TYR 0.016 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 85 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 64 time to evaluate : 0.519 Fit side-chains REVERT: D 48 PHE cc_start: 0.8383 (OUTLIER) cc_final: 0.8115 (t80) REVERT: E 80 GLU cc_start: 0.8541 (mt-10) cc_final: 0.7996 (mm-30) REVERT: E 104 LYS cc_start: 0.7918 (tttt) cc_final: 0.7169 (tmtt) REVERT: C 48 PHE cc_start: 0.8322 (OUTLIER) cc_final: 0.7920 (t80) REVERT: B 84 ASP cc_start: 0.8701 (OUTLIER) cc_final: 0.8322 (t0) REVERT: A 90 ARG cc_start: 0.8644 (ttp80) cc_final: 0.6973 (tpm170) outliers start: 21 outliers final: 17 residues processed: 74 average time/residue: 0.4004 time to fit residues: 35.9925 Evaluate side-chains 81 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 61 time to evaluate : 0.699 ------------------------------------------------------------------------------- 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 81 ASP Chi-restraints excluded: chain E residue 93 SER 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 C residue 84 ASP Chi-restraints excluded: chain B residue 84 ASP 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 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: 0.9990 chunk 43 optimal weight: 0.6980 chunk 26 optimal weight: 1.9990 chunk 3 optimal weight: 0.9990 chunk 35 optimal weight: 0.3980 chunk 9 optimal weight: 0.9980 chunk 28 optimal weight: 2.9990 chunk 5 optimal weight: 0.8980 chunk 17 optimal weight: 0.5980 chunk 12 optimal weight: 2.9990 chunk 11 optimal weight: 0.3980 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 ** 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 = 0.3821 r_free = 0.3821 target = 0.113816 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.106850 restraints weight = 21712.009| |-----------------------------------------------------------------------------| r_work (start): 0.3731 rms_B_bonded: 2.16 r_work: 0.3667 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3573 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3573 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 0.6899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 4032 Z= 0.206 Angle : 0.584 4.486 5454 Z= 0.322 Chirality : 0.044 0.126 612 Planarity : 0.004 0.032 714 Dihedral : 5.922 18.944 576 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.08 % Favored : 93.92 % Rotamer: Outliers : 4.93 % Allowed : 15.96 % Favored : 79.11 % 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 E 34 HIS 0.003 0.001 HIS A 96 PHE 0.003 0.001 PHE B 61 TYR 0.013 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 87 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 66 time to evaluate : 0.617 Fit side-chains REVERT: D 48 PHE cc_start: 0.8340 (OUTLIER) cc_final: 0.8069 (t80) REVERT: E 104 LYS cc_start: 0.7904 (tttt) cc_final: 0.7206 (tmtt) REVERT: C 48 PHE cc_start: 0.8277 (OUTLIER) cc_final: 0.7861 (t80) REVERT: A 90 ARG cc_start: 0.8520 (ttp80) cc_final: 0.7032 (tpm170) outliers start: 21 outliers final: 16 residues processed: 74 average time/residue: 0.4091 time to fit residues: 37.7884 Evaluate side-chains 81 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 63 time to evaluate : 1.962 ------------------------------------------------------------------------------- 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 81 ASP 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 F residue 84 ASP Chi-restraints excluded: chain C residue 48 PHE Chi-restraints excluded: chain C residue 84 ASP 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 22 optimal weight: 1.9990 chunk 35 optimal weight: 0.2980 chunk 36 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 3 optimal weight: 0.9980 chunk 43 optimal weight: 0.1980 chunk 0 optimal weight: 1.9990 chunk 11 optimal weight: 0.2980 chunk 12 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 39 optimal weight: 2.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- 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 = 0.3828 r_free = 0.3828 target = 0.113754 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.106838 restraints weight = 21848.091| |-----------------------------------------------------------------------------| r_work (start): 0.3747 rms_B_bonded: 2.17 r_work: 0.3674 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3581 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3581 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 moved from start: 0.6985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 4032 Z= 0.246 Angle : 0.589 4.570 5454 Z= 0.325 Chirality : 0.044 0.127 612 Planarity : 0.003 0.032 714 Dihedral : 5.909 18.661 576 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 4.69 % Allowed : 16.67 % 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: -3.54 (0.28), residues: 510 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.69 (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 0.003 0.001 PHE B 99 TYR 0.014 0.002 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: 20 poor density : 66 time to evaluate : 1.155 Fit side-chains REVERT: D 48 PHE cc_start: 0.8361 (OUTLIER) cc_final: 0.8081 (t80) REVERT: E 80 GLU cc_start: 0.8676 (OUTLIER) cc_final: 0.8083 (mm-30) REVERT: E 104 LYS cc_start: 0.7911 (tttt) cc_final: 0.7119 (tmtt) REVERT: C 48 PHE cc_start: 0.8275 (OUTLIER) cc_final: 0.7854 (t80) REVERT: A 90 ARG cc_start: 0.8445 (ttp80) cc_final: 0.6909 (tpm170) outliers start: 20 outliers final: 17 residues processed: 73 average time/residue: 0.5598 time to fit residues: 50.9518 Evaluate side-chains 83 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 63 time to evaluate : 1.001 ------------------------------------------------------------------------------- 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 81 ASP 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 C residue 84 ASP 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 84 ASP 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: 0.9980 chunk 15 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 21 optimal weight: 0.9990 chunk 35 optimal weight: 0.3980 chunk 45 optimal weight: 1.9990 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: 2.9990 overall best weight: 1.0786 ------------------------------------------------------------------------------- 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 = 0.3815 r_free = 0.3815 target = 0.112231 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.105356 restraints weight = 22056.171| |-----------------------------------------------------------------------------| r_work (start): 0.3729 rms_B_bonded: 2.17 r_work: 0.3665 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3571 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3571 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.7067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 4032 Z= 0.331 Angle : 0.639 5.975 5454 Z= 0.351 Chirality : 0.045 0.127 612 Planarity : 0.004 0.032 714 Dihedral : 6.058 18.703 576 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.69 % Favored : 94.31 % Rotamer: Outliers : 4.69 % Allowed : 17.37 % 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: -3.53 (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 0.007 0.001 TRP E 34 HIS 0.002 0.001 HIS E 96 PHE 0.003 0.001 PHE B 61 TYR 0.016 0.002 TYR F 85 ARG 0.003 0.000 ARG C 28 *********************** 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 83 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 63 time to evaluate : 0.589 Fit side-chains REVERT: D 48 PHE cc_start: 0.8375 (OUTLIER) cc_final: 0.8126 (t80) REVERT: E 80 GLU cc_start: 0.8640 (OUTLIER) cc_final: 0.8065 (mm-30) REVERT: E 104 LYS cc_start: 0.7907 (tttt) cc_final: 0.7131 (tmtt) REVERT: F 80 GLU cc_start: 0.8287 (mt-10) cc_final: 0.8004 (mt-10) REVERT: C 48 PHE cc_start: 0.8316 (OUTLIER) cc_final: 0.7907 (t80) REVERT: A 90 ARG cc_start: 0.8454 (ttp80) cc_final: 0.6886 (tpm170) outliers start: 20 outliers final: 16 residues processed: 70 average time/residue: 0.3493 time to fit residues: 30.2643 Evaluate side-chains 79 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 60 time to evaluate : 0.653 ------------------------------------------------------------------------------- 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 81 ASP 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 F residue 84 ASP Chi-restraints excluded: chain C residue 48 PHE Chi-restraints excluded: chain C residue 84 ASP 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 84 ASP Chi-restraints excluded: chain A residue 89 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: 0.8980 chunk 13 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 35 optimal weight: 0.9980 chunk 14 optimal weight: 1.9990 chunk 5 optimal weight: 0.5980 chunk 25 optimal weight: 0.5980 chunk 41 optimal weight: 0.9980 chunk 43 optimal weight: 0.6980 chunk 31 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.3828 r_free = 0.3828 target = 0.113239 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.106396 restraints weight = 22008.333| |-----------------------------------------------------------------------------| r_work (start): 0.3746 rms_B_bonded: 2.15 r_work: 0.3674 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3582 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3582 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 moved from start: 0.7121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 4032 Z= 0.250 Angle : 0.608 5.348 5454 Z= 0.331 Chirality : 0.044 0.125 612 Planarity : 0.003 0.032 714 Dihedral : 5.930 18.730 576 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 4.23 % Allowed : 18.31 % Favored : 77.46 % 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: -3.51 (0.28), residues: 510 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.67 (0.21), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 34 HIS 0.003 0.001 HIS F 96 PHE 0.005 0.001 PHE A 48 TYR 0.015 0.001 TYR F 86 ARG 0.002 0.000 ARG B 90 ********************** 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 80 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 62 time to evaluate : 0.695 Fit side-chains REVERT: D 48 PHE cc_start: 0.8332 (OUTLIER) cc_final: 0.8056 (t80) REVERT: E 80 GLU cc_start: 0.8663 (OUTLIER) cc_final: 0.8001 (mm-30) REVERT: E 104 LYS cc_start: 0.7889 (tttt) cc_final: 0.7104 (tmtt) REVERT: F 80 GLU cc_start: 0.8351 (mt-10) cc_final: 0.8065 (mt-10) REVERT: C 48 PHE cc_start: 0.8276 (OUTLIER) cc_final: 0.7871 (t80) REVERT: A 90 ARG cc_start: 0.8479 (ttp80) cc_final: 0.6972 (tpm170) outliers start: 18 outliers final: 15 residues processed: 67 average time/residue: 0.3284 time to fit residues: 27.7331 Evaluate side-chains 78 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 60 time to evaluate : 0.610 ------------------------------------------------------------------------------- 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 C residue 84 ASP 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 84 ASP Chi-restraints excluded: chain A residue 89 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: 0.9980 chunk 24 optimal weight: 1.9990 chunk 16 optimal weight: 0.7980 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: 0.5980 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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 = 0.3828 r_free = 0.3828 target = 0.113166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.106418 restraints weight = 21573.082| |-----------------------------------------------------------------------------| r_work (start): 0.3735 rms_B_bonded: 2.10 r_work: 0.3664 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3571 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3571 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 moved from start: 0.7161 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= 0.265 Angle : 0.613 5.557 5454 Z= 0.334 Chirality : 0.044 0.124 612 Planarity : 0.003 0.031 714 Dihedral : 5.935 18.521 576 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 4.46 % Allowed : 18.54 % Favored : 77.00 % 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: -3.51 (0.28), residues: 510 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.67 (0.21), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 34 HIS 0.002 0.001 HIS A 96 PHE 0.003 0.001 PHE E 99 TYR 0.014 0.002 TYR F 85 ARG 0.002 0.000 ARG B 90 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4865.39 seconds wall clock time: 86 minutes 33.45 seconds (5193.45 seconds total)