Starting phenix.real_space_refine on Fri Jul 25 13:41:54 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6z1o_11031/07_2025/6z1o_11031.cif Found real_map, /net/cci-nas-00/data/ceres_data/6z1o_11031/07_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_11031/07_2025/6z1o_11031.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6z1o_11031/07_2025/6z1o_11031.map" model { file = "/net/cci-nas-00/data/ceres_data/6z1o_11031/07_2025/6z1o_11031.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6z1o_11031/07_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-5711/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: 3.31, per 1000 atoms: 0.43 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: 1.90 Conformation dependent library (CDL) restraints added in 768.9 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: 1.03 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: 3.07 Time building geometry restraints manager: 2.35 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: 1.710 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: 0.160 Extract box with map and model: 0.350 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 20.850 Find NCS groups from input model: 0.120 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:2.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.340 ------------------------------------------------------------------------------- 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 4033 Z= 0.957 Angle : 2.231 9.468 5456 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 Details of bonding type rmsd hydrogen bonds : bond 0.11912 ( 185) hydrogen bonds : angle 7.23459 ( 555) SS BOND : bond 0.03856 ( 1) SS BOND : angle 3.72000 ( 2) covalent geometry : bond 0.01336 ( 4032) covalent geometry : angle 2.23067 ( 5454) *********************** 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: 0.4615 time to fit residues: 86.9335 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 : 0.661 ------------------------------------------------------------------------------- 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: 0.7980 chunk 22 optimal weight: 0.5980 chunk 28 optimal weight: 1.9990 chunk 43 optimal weight: 0.2980 overall best weight: 0.5180 ------------------------------------------------------------------------------- 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 = 0.4019 r_free = 0.4019 target = 0.128511 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.120422 restraints weight = 20253.981| |-----------------------------------------------------------------------------| r_work (start): 0.3918 rms_B_bonded: 2.13 r_work: 0.3847 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3751 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3751 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7787 moved from start: 0.4260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 4033 Z= 0.155 Angle : 0.653 4.435 5456 Z= 0.368 Chirality : 0.047 0.133 612 Planarity : 0.005 0.042 714 Dihedral : 6.384 19.422 576 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 1.88 % Allowed : 16.67 % Favored : 81.46 % 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: -3.68 (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 0.011 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 90 Details of bonding type rmsd hydrogen bonds : bond 0.02906 ( 185) hydrogen bonds : angle 5.86042 ( 555) SS BOND : bond 0.00283 ( 1) SS BOND : angle 0.41851 ( 2) covalent geometry : bond 0.00336 ( 4032) covalent geometry : angle 0.65328 ( 5454) *********************** 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 : 0.681 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 104 LYS cc_start: 0.7764 (tttt) cc_final: 0.7106 (tmtt) REVERT: C 46 VAL cc_start: 0.9179 (m) cc_final: 0.8916 (t) REVERT: C 49 ARG cc_start: 0.6341 (tpt90) cc_final: 0.5878 (tpt90) REVERT: B 48 PHE cc_start: 0.8581 (m-80) cc_final: 0.8284 (m-80) REVERT: B 97 GLN cc_start: 0.8980 (mp10) cc_final: 0.8619 (mt0) REVERT: A 19 ARG cc_start: 0.8411 (ttt180) cc_final: 0.7298 (mmp-170) REVERT: A 23 GLN cc_start: 0.7809 (tt0) cc_final: 0.7596 (tt0) REVERT: A 34 TRP cc_start: 0.8137 (t-100) cc_final: 0.6951 (t60) REVERT: A 104 LYS cc_start: 0.7687 (tttt) cc_final: 0.7161 (tttm) outliers start: 8 outliers final: 5 residues processed: 103 average time/residue: 0.3415 time to fit residues: 44.2581 Evaluate side-chains 83 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 78 time to evaluate : 0.637 ------------------------------------------------------------------------------- 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: 0.9980 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: 0.6980 chunk 31 optimal weight: 2.9990 chunk 19 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3782 r_free = 0.3782 target = 0.112497 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.105439 restraints weight = 21794.707| |-----------------------------------------------------------------------------| r_work (start): 0.3693 rms_B_bonded: 2.06 r_work: 0.3622 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3532 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.3532 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 moved from start: 0.5759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.033 4033 Z= 0.276 Angle : 0.712 4.942 5456 Z= 0.399 Chirality : 0.047 0.135 612 Planarity : 0.005 0.038 714 Dihedral : 6.452 17.444 576 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 10.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 3.52 % Allowed : 17.37 % 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: -3.70 (0.27), residues: 510 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.82 (0.21), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.003 TRP E 34 HIS 0.002 0.001 HIS E 96 PHE 0.010 0.001 PHE F 99 TYR 0.024 0.003 TYR F 85 ARG 0.003 0.001 ARG A 60 Details of bonding type rmsd hydrogen bonds : bond 0.03258 ( 185) hydrogen bonds : angle 5.10297 ( 555) SS BOND : bond 0.01541 ( 1) SS BOND : angle 1.88890 ( 2) covalent geometry : bond 0.00627 ( 4032) covalent geometry : angle 0.71157 ( 5454) *********************** 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 90 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 75 time to evaluate : 0.617 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 48 PHE cc_start: 0.8378 (OUTLIER) cc_final: 0.8119 (t80) REVERT: E 80 GLU cc_start: 0.8451 (OUTLIER) cc_final: 0.7918 (mm-30) REVERT: C 48 PHE cc_start: 0.8367 (OUTLIER) cc_final: 0.7926 (t80) REVERT: B 48 PHE cc_start: 0.8714 (m-80) cc_final: 0.8505 (m-80) REVERT: B 84 ASP cc_start: 0.8949 (OUTLIER) cc_final: 0.8225 (t0) REVERT: B 97 GLN cc_start: 0.9108 (mp10) cc_final: 0.8793 (mt0) REVERT: A 90 ARG cc_start: 0.8598 (ttp80) cc_final: 0.6770 (tpm170) outliers start: 15 outliers final: 8 residues processed: 81 average time/residue: 0.3730 time to fit residues: 37.1787 Evaluate side-chains 76 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 64 time to evaluate : 0.681 ------------------------------------------------------------------------------- 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 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 84 ASP Chi-restraints excluded: chain B residue 93 SER Chi-restraints excluded: chain A residue 71 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 22 optimal weight: 0.9990 chunk 30 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 33 optimal weight: 0.5980 chunk 9 optimal weight: 1.9990 chunk 5 optimal weight: 0.9990 chunk 40 optimal weight: 0.9990 chunk 1 optimal weight: 0.5980 chunk 16 optimal weight: 0.9980 chunk 44 optimal weight: 1.9990 chunk 27 optimal weight: 0.3980 overall best weight: 0.7182 ------------------------------------------------------------------------------- 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 = 0.3816 r_free = 0.3816 target = 0.114204 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.106962 restraints weight = 21698.636| |-----------------------------------------------------------------------------| r_work (start): 0.3726 rms_B_bonded: 2.14 r_work: 0.3653 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3560 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3560 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.6178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 4033 Z= 0.159 Angle : 0.603 4.458 5456 Z= 0.335 Chirality : 0.045 0.135 612 Planarity : 0.004 0.035 714 Dihedral : 6.131 16.586 576 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 3.52 % Allowed : 18.54 % 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: -3.62 (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 0.002 0.001 HIS F 96 PHE 0.005 0.001 PHE A 48 TYR 0.016 0.002 TYR F 86 ARG 0.003 0.000 ARG D 49 Details of bonding type rmsd hydrogen bonds : bond 0.02696 ( 185) hydrogen bonds : angle 4.76355 ( 555) SS BOND : bond 0.00637 ( 1) SS BOND : angle 0.81001 ( 2) covalent geometry : bond 0.00356 ( 4032) covalent geometry : angle 0.60281 ( 5454) *********************** 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 87 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 72 time to evaluate : 0.611 Fit side-chains revert: symmetry clash REVERT: D 48 PHE cc_start: 0.8340 (OUTLIER) cc_final: 0.8095 (t80) REVERT: D 80 GLU cc_start: 0.8289 (mt-10) cc_final: 0.8071 (mt-10) REVERT: E 80 GLU cc_start: 0.8533 (mt-10) cc_final: 0.8300 (mm-30) REVERT: E 104 LYS cc_start: 0.7843 (tttt) cc_final: 0.7186 (tmtt) REVERT: C 48 PHE cc_start: 0.8267 (OUTLIER) cc_final: 0.7826 (t80) REVERT: B 97 GLN cc_start: 0.9124 (mp10) cc_final: 0.8835 (mt0) REVERT: A 25 ASP cc_start: 0.7861 (p0) cc_final: 0.7638 (p0) REVERT: A 90 ARG cc_start: 0.8522 (ttp80) cc_final: 0.6821 (tpm170) outliers start: 15 outliers final: 10 residues processed: 76 average time/residue: 0.3337 time to fit residues: 31.6912 Evaluate side-chains 76 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 64 time to evaluate : 0.604 ------------------------------------------------------------------------------- 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 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 A residue 71 SER Chi-restraints excluded: chain A residue 88 ASN 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: 0.9990 chunk 5 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 23 optimal weight: 0.9980 chunk 29 optimal weight: 0.6980 chunk 3 optimal weight: 0.2980 chunk 30 optimal weight: 0.9980 chunk 40 optimal weight: 1.9990 chunk 0 optimal weight: 0.9990 chunk 46 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 = 0.3818 r_free = 0.3818 target = 0.113430 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.106160 restraints weight = 21621.091| |-----------------------------------------------------------------------------| r_work (start): 0.3726 rms_B_bonded: 2.18 r_work: 0.3658 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3562 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3562 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 moved from start: 0.6422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 4033 Z= 0.176 Angle : 0.601 4.632 5456 Z= 0.333 Chirality : 0.044 0.133 612 Planarity : 0.004 0.034 714 Dihedral : 6.045 16.599 576 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 4.23 % Allowed : 17.84 % 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: -3.62 (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 Details of bonding type rmsd hydrogen bonds : bond 0.02650 ( 185) hydrogen bonds : angle 4.59720 ( 555) SS BOND : bond 0.00653 ( 1) SS BOND : angle 0.82151 ( 2) covalent geometry : bond 0.00398 ( 4032) covalent geometry : angle 0.60113 ( 5454) *********************** 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: 18 poor density : 68 time to evaluate : 0.637 Fit side-chains revert: symmetry clash REVERT: D 48 PHE cc_start: 0.8326 (OUTLIER) cc_final: 0.8061 (t80) REVERT: E 80 GLU cc_start: 0.8524 (mt-10) cc_final: 0.8273 (mm-30) REVERT: E 104 LYS cc_start: 0.7861 (tttt) cc_final: 0.7204 (tmtt) REVERT: C 48 PHE cc_start: 0.8291 (OUTLIER) cc_final: 0.7864 (t80) REVERT: B 97 GLN cc_start: 0.9130 (mp10) cc_final: 0.8866 (mt0) REVERT: A 90 ARG cc_start: 0.8534 (ttp80) cc_final: 0.6830 (tpm170) outliers start: 18 outliers final: 14 residues processed: 75 average time/residue: 0.3119 time to fit residues: 30.5025 Evaluate side-chains 80 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 64 time to evaluate : 0.628 ------------------------------------------------------------------------------- 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 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: 2.9990 chunk 45 optimal weight: 0.9990 chunk 42 optimal weight: 0.9980 chunk 23 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 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: 0.9980 chunk 47 optimal weight: 1.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- 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 = 0.3777 r_free = 0.3777 target = 0.110736 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.103619 restraints weight = 21981.416| |-----------------------------------------------------------------------------| r_work (start): 0.3682 rms_B_bonded: 2.13 r_work: 0.3616 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3521 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3521 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.6736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.031 4033 Z= 0.249 Angle : 0.648 4.804 5456 Z= 0.361 Chirality : 0.045 0.131 612 Planarity : 0.004 0.034 714 Dihedral : 6.200 18.941 576 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 3.99 % Allowed : 17.84 % 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: -3.69 (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 0.010 0.002 TRP E 34 HIS 0.003 0.001 HIS F 96 PHE 0.004 0.001 PHE F 99 TYR 0.017 0.002 TYR F 85 ARG 0.004 0.001 ARG D 49 Details of bonding type rmsd hydrogen bonds : bond 0.03004 ( 185) hydrogen bonds : angle 4.61570 ( 555) SS BOND : bond 0.00890 ( 1) SS BOND : angle 1.11581 ( 2) covalent geometry : bond 0.00564 ( 4032) covalent geometry : angle 0.64760 ( 5454) *********************** 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 81 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 64 time to evaluate : 0.577 Fit side-chains REVERT: D 48 PHE cc_start: 0.8389 (OUTLIER) cc_final: 0.8120 (t80) REVERT: E 80 GLU cc_start: 0.8554 (mt-10) cc_final: 0.8096 (mm-30) REVERT: E 104 LYS cc_start: 0.7963 (tttt) cc_final: 0.7274 (tmtt) REVERT: C 48 PHE cc_start: 0.8339 (OUTLIER) cc_final: 0.7937 (t80) REVERT: A 90 ARG cc_start: 0.8587 (ttp80) cc_final: 0.6862 (tpm170) outliers start: 17 outliers final: 13 residues processed: 70 average time/residue: 0.4402 time to fit residues: 39.9812 Evaluate side-chains 77 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 62 time to evaluate : 0.718 ------------------------------------------------------------------------------- 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 33 optimal weight: 0.9990 chunk 43 optimal weight: 0.0870 chunk 26 optimal weight: 1.9990 chunk 3 optimal weight: 0.9980 chunk 35 optimal weight: 0.3980 chunk 9 optimal weight: 0.8980 chunk 28 optimal weight: 2.9990 chunk 5 optimal weight: 0.9990 chunk 17 optimal weight: 0.8980 chunk 12 optimal weight: 2.9990 chunk 11 optimal weight: 0.5980 overall best weight: 0.5758 ------------------------------------------------------------------------------- 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 = 0.3850 r_free = 0.3850 target = 0.115443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.108176 restraints weight = 21339.137| |-----------------------------------------------------------------------------| r_work (start): 0.3764 rms_B_bonded: 2.22 r_work: 0.3699 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3601 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3601 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8004 moved from start: 0.6843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4033 Z= 0.137 Angle : 0.575 5.022 5456 Z= 0.317 Chirality : 0.044 0.128 612 Planarity : 0.003 0.032 714 Dihedral : 5.906 18.341 576 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 3.99 % Allowed : 18.31 % Favored : 77.70 % 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 0.007 0.001 TRP E 34 HIS 0.003 0.002 HIS A 96 PHE 0.003 0.001 PHE B 61 TYR 0.012 0.001 TYR F 86 ARG 0.002 0.000 ARG D 49 Details of bonding type rmsd hydrogen bonds : bond 0.02521 ( 185) hydrogen bonds : angle 4.50404 ( 555) SS BOND : bond 0.00443 ( 1) SS BOND : angle 0.70531 ( 2) covalent geometry : bond 0.00311 ( 4032) covalent geometry : angle 0.57512 ( 5454) *********************** 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: 17 poor density : 68 time to evaluate : 0.751 Fit side-chains REVERT: D 48 PHE cc_start: 0.8323 (OUTLIER) cc_final: 0.8071 (t80) REVERT: E 104 LYS cc_start: 0.7928 (tttt) cc_final: 0.7263 (tmtt) REVERT: C 48 PHE cc_start: 0.8282 (OUTLIER) cc_final: 0.7879 (t80) REVERT: A 90 ARG cc_start: 0.8594 (ttp80) cc_final: 0.6934 (tpm170) outliers start: 17 outliers final: 12 residues processed: 73 average time/residue: 0.4644 time to fit residues: 42.5912 Evaluate side-chains 78 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 64 time to evaluate : 0.662 ------------------------------------------------------------------------------- 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 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 A residue 34 TRP Chi-restraints excluded: chain A residue 71 SER Chi-restraints excluded: chain A residue 89 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 22 optimal weight: 0.7980 chunk 35 optimal weight: 0.9990 chunk 36 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 3 optimal weight: 0.9980 chunk 43 optimal weight: 0.6980 chunk 0 optimal weight: 1.9990 chunk 11 optimal weight: 0.1980 chunk 12 optimal weight: 2.9990 chunk 30 optimal weight: 0.9980 chunk 39 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3830 r_free = 0.3830 target = 0.114136 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.107138 restraints weight = 21941.459| |-----------------------------------------------------------------------------| r_work (start): 0.3741 rms_B_bonded: 2.17 r_work: 0.3676 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3583 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.3583 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 moved from start: 0.6978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 4033 Z= 0.166 Angle : 0.595 4.616 5456 Z= 0.326 Chirality : 0.044 0.126 612 Planarity : 0.003 0.032 714 Dihedral : 5.890 17.705 576 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 4.46 % Allowed : 18.78 % Favored : 76.76 % 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: -3.57 (0.27), residues: 510 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.71 (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 A 96 PHE 0.004 0.001 PHE E 48 TYR 0.013 0.002 TYR F 85 ARG 0.002 0.000 ARG D 49 Details of bonding type rmsd hydrogen bonds : bond 0.02545 ( 185) hydrogen bonds : angle 4.48048 ( 555) SS BOND : bond 0.00646 ( 1) SS BOND : angle 0.88854 ( 2) covalent geometry : bond 0.00381 ( 4032) covalent geometry : angle 0.59438 ( 5454) *********************** 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 83 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 64 time to evaluate : 1.861 Fit side-chains REVERT: D 48 PHE cc_start: 0.8337 (OUTLIER) cc_final: 0.8071 (t80) REVERT: E 104 LYS cc_start: 0.7940 (tttt) cc_final: 0.7272 (tmtt) REVERT: F 80 GLU cc_start: 0.8294 (mt-10) cc_final: 0.8019 (mt-10) REVERT: C 48 PHE cc_start: 0.8297 (OUTLIER) cc_final: 0.7884 (t80) REVERT: A 90 ARG cc_start: 0.8509 (ttp80) cc_final: 0.6991 (tpm170) outliers start: 19 outliers final: 15 residues processed: 70 average time/residue: 0.4417 time to fit residues: 40.4457 Evaluate side-chains 79 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 62 time to evaluate : 0.750 ------------------------------------------------------------------------------- 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 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 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: 1.9990 chunk 15 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 35 optimal weight: 0.9990 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: 2.9990 overall best weight: 1.3990 ------------------------------------------------------------------------------- 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 = 0.3784 r_free = 0.3784 target = 0.110739 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.103771 restraints weight = 21994.283| |-----------------------------------------------------------------------------| r_work (start): 0.3694 rms_B_bonded: 2.15 r_work: 0.3624 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3531 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3531 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 moved from start: 0.7068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.036 4033 Z= 0.282 Angle : 0.673 4.895 5456 Z= 0.372 Chirality : 0.046 0.129 612 Planarity : 0.004 0.033 714 Dihedral : 6.206 16.826 576 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.08 % Favored : 93.92 % Rotamer: Outliers : 4.46 % Allowed : 19.01 % Favored : 76.53 % 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 : -2.74 (0.21), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP E 34 HIS 0.003 0.001 HIS E 96 PHE 0.004 0.001 PHE B 61 TYR 0.018 0.002 TYR F 85 ARG 0.003 0.001 ARG D 49 Details of bonding type rmsd hydrogen bonds : bond 0.03046 ( 185) hydrogen bonds : angle 4.63742 ( 555) SS BOND : bond 0.00944 ( 1) SS BOND : angle 1.11133 ( 2) covalent geometry : bond 0.00636 ( 4032) covalent geometry : angle 0.67297 ( 5454) *********************** 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 82 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 63 time to evaluate : 0.604 Fit side-chains REVERT: D 48 PHE cc_start: 0.8430 (OUTLIER) cc_final: 0.8162 (t80) REVERT: E 80 GLU cc_start: 0.8664 (OUTLIER) cc_final: 0.8370 (mm-30) REVERT: E 104 LYS cc_start: 0.8010 (tttt) cc_final: 0.7245 (tmtt) REVERT: F 80 GLU cc_start: 0.8300 (mt-10) cc_final: 0.7986 (mt-10) REVERT: C 48 PHE cc_start: 0.8373 (OUTLIER) cc_final: 0.7963 (t80) REVERT: A 90 ARG cc_start: 0.8513 (ttp80) cc_final: 0.6965 (tpm170) outliers start: 19 outliers final: 13 residues processed: 71 average time/residue: 0.3419 time to fit residues: 30.1716 Evaluate side-chains 73 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 57 time to evaluate : 0.642 ------------------------------------------------------------------------------- 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 84 ASP Chi-restraints excluded: chain C residue 48 PHE 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 1 optimal weight: 0.9990 chunk 29 optimal weight: 1.9990 chunk 13 optimal weight: 0.9980 chunk 28 optimal weight: 2.9990 chunk 35 optimal weight: 0.8980 chunk 14 optimal weight: 1.9990 chunk 5 optimal weight: 0.5980 chunk 25 optimal weight: 0.5980 chunk 41 optimal weight: 0.7980 chunk 43 optimal weight: 0.2980 chunk 31 optimal weight: 1.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3839 r_free = 0.3839 target = 0.114415 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.107508 restraints weight = 21723.274| |-----------------------------------------------------------------------------| r_work (start): 0.3749 rms_B_bonded: 2.12 r_work: 0.3686 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3594 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3594 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 moved from start: 0.7135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 4033 Z= 0.154 Angle : 0.605 5.433 5456 Z= 0.329 Chirality : 0.044 0.126 612 Planarity : 0.004 0.031 714 Dihedral : 5.929 16.727 576 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 3.52 % Allowed : 20.89 % Favored : 75.59 % 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 0.004 0.001 TRP B 34 HIS 0.003 0.002 HIS A 96 PHE 0.005 0.001 PHE A 48 TYR 0.014 0.001 TYR F 86 ARG 0.002 0.000 ARG E 49 Details of bonding type rmsd hydrogen bonds : bond 0.02584 ( 185) hydrogen bonds : angle 4.53008 ( 555) SS BOND : bond 0.00395 ( 1) SS BOND : angle 0.79193 ( 2) covalent geometry : bond 0.00351 ( 4032) covalent geometry : angle 0.60536 ( 5454) ********************** 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 : 0.601 Fit side-chains REVERT: D 48 PHE cc_start: 0.8309 (OUTLIER) cc_final: 0.8101 (t80) REVERT: E 80 GLU cc_start: 0.8657 (mm-30) cc_final: 0.8256 (mm-30) REVERT: E 104 LYS cc_start: 0.7910 (tttt) cc_final: 0.7201 (tmtt) REVERT: F 80 GLU cc_start: 0.8289 (mt-10) cc_final: 0.7983 (mt-10) REVERT: C 48 PHE cc_start: 0.8299 (OUTLIER) cc_final: 0.7931 (t80) REVERT: A 90 ARG cc_start: 0.8444 (ttp80) cc_final: 0.7080 (tpm170) outliers start: 15 outliers final: 13 residues processed: 76 average time/residue: 0.3302 time to fit residues: 31.1773 Evaluate side-chains 79 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 64 time to evaluate : 0.594 ------------------------------------------------------------------------------- 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 C residue 48 PHE 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 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: 0.4980 chunk 28 optimal weight: 2.9990 chunk 1 optimal weight: 0.9990 chunk 10 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 21 optimal weight: 0.9980 overall best weight: 1.0986 ------------------------------------------------------------------------------- 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 = 0.3795 r_free = 0.3795 target = 0.111888 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.105035 restraints weight = 21764.627| |-----------------------------------------------------------------------------| r_work (start): 0.3702 rms_B_bonded: 2.12 r_work: 0.3640 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3547 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.3547 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 0.7182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.031 4033 Z= 0.229 Angle : 0.651 5.839 5456 Z= 0.355 Chirality : 0.045 0.124 612 Planarity : 0.004 0.031 714 Dihedral : 6.046 16.473 576 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 3.76 % Allowed : 20.42 % Favored : 75.82 % 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 0.008 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 0.002 0.000 ARG C 28 Details of bonding type rmsd hydrogen bonds : bond 0.02801 ( 185) hydrogen bonds : angle 4.57012 ( 555) SS BOND : bond 0.00763 ( 1) SS BOND : angle 1.00708 ( 2) covalent geometry : bond 0.00520 ( 4032) covalent geometry : angle 0.65070 ( 5454) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4966.59 seconds wall clock time: 87 minutes 43.72 seconds (5263.72 seconds total)