Starting phenix.real_space_refine on Wed Mar 12 19:49:21 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7nsl_12570/03_2025/7nsl_12570.cif Found real_map, /net/cci-nas-00/data/ceres_data/7nsl_12570/03_2025/7nsl_12570.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7nsl_12570/03_2025/7nsl_12570.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7nsl_12570/03_2025/7nsl_12570.map" model { file = "/net/cci-nas-00/data/ceres_data/7nsl_12570/03_2025/7nsl_12570.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7nsl_12570/03_2025/7nsl_12570.cif" } resolution = 3.1 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 14 5.16 5 C 2667 2.51 5 N 679 2.21 5 O 910 1.98 5 H 4053 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 21 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: 8323 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 1189 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 1189 Classifications: {'peptide': 85} Link IDs: {'PTRANS': 3, 'TRANS': 81} Chain breaks: 1 Restraints were copied for chains: C, B, E, D, G, F Time building chain proxies: 3.05, per 1000 atoms: 0.37 Number of scatterers: 8323 At special positions: 0 Unit cell: (64.48, 98.8, 58.24, 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 14 16.00 O 910 8.00 N 679 7.00 C 2667 6.00 H 4053 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 89 " distance=2.02 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: 1.98 Conformation dependent library (CDL) restraints added in 708.2 milliseconds 1134 Ramachandran restraints generated. 567 Oldfield, 0 Emsley, 567 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1022 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 11 sheets defined 0.0% alpha, 37.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.00 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 10 through 12 Processing sheet with id=AA2, first strand: chain 'A' and resid 14 through 21 Processing sheet with id=AA3, first strand: chain 'A' and resid 31 through 34 Processing sheet with id=AA4, first strand: chain 'A' and resid 37 through 39 Processing sheet with id=AA5, first strand: chain 'A' and resid 43 through 44 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 43 through 44 current: chain 'B' and resid 43 through 44 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 43 through 44 current: chain 'C' and resid 43 through 44 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 43 through 44 current: chain 'D' and resid 43 through 44 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 43 through 44 current: chain 'E' and resid 43 through 44 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 43 through 44 current: chain 'F' and resid 43 through 44 No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 45 through 51 Processing sheet with id=AA7, first strand: chain 'A' and resid 70 through 74 Processing sheet with id=AA8, first strand: chain 'A' and resid 76 through 78 Processing sheet with id=AA9, first strand: chain 'A' and resid 88 through 89 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 88 through 89 current: chain 'B' and resid 88 through 89 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 88 through 89 current: chain 'C' and resid 88 through 89 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 88 through 89 current: chain 'D' and resid 88 through 89 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 88 through 89 current: chain 'E' and resid 88 through 89 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 88 through 89 current: chain 'F' and resid 88 through 89 No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'A' and resid 91 through 93 Processing sheet with id=AB2, first strand: chain 'A' and resid 105 through 107 180 hydrogen bonds defined for protein. 540 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: 3.03 Time building geometry restraints manager: 2.44 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 4053 1.03 - 1.23: 125 1.23 - 1.42: 1730 1.42 - 1.61: 2478 1.61 - 1.81: 14 Bond restraints: 8400 Sorted by residual: bond pdb=" CA ALA G 44 " pdb=" CB ALA G 44 " ideal model delta sigma weight residual 1.528 1.441 0.087 1.17e-02 7.31e+03 5.56e+01 bond pdb=" CA ALA A 44 " pdb=" CB ALA A 44 " ideal model delta sigma weight residual 1.528 1.441 0.087 1.17e-02 7.31e+03 5.56e+01 bond pdb=" CA ALA B 44 " pdb=" CB ALA B 44 " ideal model delta sigma weight residual 1.528 1.442 0.087 1.17e-02 7.31e+03 5.48e+01 bond pdb=" CA ALA E 44 " pdb=" CB ALA E 44 " ideal model delta sigma weight residual 1.528 1.442 0.087 1.17e-02 7.31e+03 5.47e+01 bond pdb=" CA ALA F 44 " pdb=" CB ALA F 44 " ideal model delta sigma weight residual 1.528 1.442 0.086 1.17e-02 7.31e+03 5.46e+01 ... (remaining 8395 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.12: 13451 2.12 - 4.23: 1160 4.23 - 6.35: 328 6.35 - 8.47: 104 8.47 - 10.58: 14 Bond angle restraints: 15057 Sorted by residual: angle pdb=" CA GLY G 90 " pdb=" C GLY G 90 " pdb=" O GLY G 90 " ideal model delta sigma weight residual 120.91 114.30 6.61 6.90e-01 2.10e+00 9.18e+01 angle pdb=" CA GLY C 90 " pdb=" C GLY C 90 " pdb=" O GLY C 90 " ideal model delta sigma weight residual 120.91 114.34 6.57 6.90e-01 2.10e+00 9.06e+01 angle pdb=" CA GLY E 90 " pdb=" C GLY E 90 " pdb=" O GLY E 90 " ideal model delta sigma weight residual 120.91 114.35 6.56 6.90e-01 2.10e+00 9.03e+01 angle pdb=" CA GLY B 90 " pdb=" C GLY B 90 " pdb=" O GLY B 90 " ideal model delta sigma weight residual 120.91 114.36 6.55 6.90e-01 2.10e+00 9.01e+01 angle pdb=" CA GLY F 90 " pdb=" C GLY F 90 " pdb=" O GLY F 90 " ideal model delta sigma weight residual 120.91 114.37 6.54 6.90e-01 2.10e+00 8.97e+01 ... (remaining 15052 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.17: 3438 16.17 - 32.34: 401 32.34 - 48.51: 105 48.51 - 64.68: 91 64.68 - 80.86: 7 Dihedral angle restraints: 4042 sinusoidal: 2145 harmonic: 1897 Sorted by residual: dihedral pdb=" N LEU F 97 " pdb=" CA LEU F 97 " pdb=" CB LEU F 97 " pdb=" CG LEU F 97 " ideal model delta sinusoidal sigma weight residual -60.00 -113.63 53.63 3 1.50e+01 4.44e-03 9.22e+00 dihedral pdb=" N LEU C 97 " pdb=" CA LEU C 97 " pdb=" CB LEU C 97 " pdb=" CG LEU C 97 " ideal model delta sinusoidal sigma weight residual -60.00 -113.61 53.61 3 1.50e+01 4.44e-03 9.22e+00 dihedral pdb=" N LEU B 97 " pdb=" CA LEU B 97 " pdb=" CB LEU B 97 " pdb=" CG LEU B 97 " ideal model delta sinusoidal sigma weight residual -60.00 -113.61 53.61 3 1.50e+01 4.44e-03 9.22e+00 ... (remaining 4039 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 390 0.056 - 0.111: 188 0.111 - 0.167: 67 0.167 - 0.222: 34 0.222 - 0.278: 14 Chirality restraints: 693 Sorted by residual: chirality pdb=" CA LEU A 47 " pdb=" N LEU A 47 " pdb=" C LEU A 47 " pdb=" CB LEU A 47 " both_signs ideal model delta sigma weight residual False 2.51 2.79 -0.28 2.00e-01 2.50e+01 1.93e+00 chirality pdb=" CA LEU B 47 " pdb=" N LEU B 47 " pdb=" C LEU B 47 " pdb=" CB LEU B 47 " both_signs ideal model delta sigma weight residual False 2.51 2.79 -0.28 2.00e-01 2.50e+01 1.92e+00 chirality pdb=" CA LEU F 47 " pdb=" N LEU F 47 " pdb=" C LEU F 47 " pdb=" CB LEU F 47 " both_signs ideal model delta sigma weight residual False 2.51 2.79 -0.28 2.00e-01 2.50e+01 1.90e+00 ... (remaining 690 not shown) Planarity restraints: 1309 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLN E 16 " -0.240 2.00e-02 2.50e+03 3.43e-01 1.77e+03 pdb=" CD GLN E 16 " 0.009 2.00e-02 2.50e+03 pdb=" OE1 GLN E 16 " 0.236 2.00e-02 2.50e+03 pdb=" NE2 GLN E 16 " -0.004 2.00e-02 2.50e+03 pdb="HE21 GLN E 16 " 0.544 2.00e-02 2.50e+03 pdb="HE22 GLN E 16 " -0.546 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN G 16 " -0.240 2.00e-02 2.50e+03 3.43e-01 1.77e+03 pdb=" CD GLN G 16 " 0.009 2.00e-02 2.50e+03 pdb=" OE1 GLN G 16 " 0.236 2.00e-02 2.50e+03 pdb=" NE2 GLN G 16 " -0.004 2.00e-02 2.50e+03 pdb="HE21 GLN G 16 " 0.544 2.00e-02 2.50e+03 pdb="HE22 GLN G 16 " -0.546 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN D 16 " -0.240 2.00e-02 2.50e+03 3.43e-01 1.77e+03 pdb=" CD GLN D 16 " 0.009 2.00e-02 2.50e+03 pdb=" OE1 GLN D 16 " 0.236 2.00e-02 2.50e+03 pdb=" NE2 GLN D 16 " -0.004 2.00e-02 2.50e+03 pdb="HE21 GLN D 16 " 0.544 2.00e-02 2.50e+03 pdb="HE22 GLN D 16 " -0.546 2.00e-02 2.50e+03 ... (remaining 1306 not shown) Histogram of nonbonded interaction distances: 1.57 - 2.18: 433 2.18 - 2.78: 16305 2.78 - 3.39: 22348 3.39 - 3.99: 32827 3.99 - 4.60: 47613 Nonbonded interactions: 119526 Sorted by model distance: nonbonded pdb=" HG1 THR A 81 " pdb=" OD1 ASP A 83 " model vdw 1.572 2.450 nonbonded pdb=" HG1 THR E 81 " pdb=" OD1 ASP E 83 " model vdw 1.573 2.450 nonbonded pdb=" HG1 THR F 81 " pdb=" OD1 ASP F 83 " model vdw 1.573 2.450 nonbonded pdb=" HG1 THR G 81 " pdb=" OD1 ASP G 83 " model vdw 1.573 2.450 nonbonded pdb=" HG1 THR D 81 " pdb=" OD1 ASP D 83 " model vdw 1.573 2.450 ... (remaining 119521 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: 0.05 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' selection = chain 'G' 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: 1.240 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: 0.150 Extract box with map and model: 0.290 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 20.900 Find NCS groups from input model: 0.150 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:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7710 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 : 0.012 0.087 4347 Z= 0.823 Angle : 1.845 8.934 5929 Z= 1.282 Chirality : 0.084 0.278 693 Planarity : 0.014 0.039 749 Dihedral : 14.483 80.856 1442 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 0.00 % Allowed : 9.09 % Favored : 90.91 % 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: -5.51 (0.17), residues: 567 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.19 (0.13), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP D 36 PHE 0.018 0.006 PHE C 101 TYR 0.024 0.002 TYR E 88 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1134 Ramachandran restraints generated. 567 Oldfield, 0 Emsley, 567 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1134 Ramachandran restraints generated. 567 Oldfield, 0 Emsley, 567 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 197 time to evaluate : 0.701 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 38 GLN cc_start: 0.9084 (pt0) cc_final: 0.8778 (pt0) REVERT: C 48 LEU cc_start: 0.8864 (mp) cc_final: 0.8451 (mp) outliers start: 0 outliers final: 0 residues processed: 197 average time/residue: 0.2375 time to fit residues: 63.0553 Evaluate side-chains 153 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 153 time to evaluate : 0.628 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 47 optimal weight: 1.9990 chunk 42 optimal weight: 0.9990 chunk 23 optimal weight: 1.9990 chunk 14 optimal weight: 0.9980 chunk 28 optimal weight: 1.9990 chunk 22 optimal weight: 0.6980 chunk 43 optimal weight: 0.9990 chunk 16 optimal weight: 1.9990 chunk 26 optimal weight: 0.9980 chunk 32 optimal weight: 0.8980 chunk 50 optimal weight: 0.9980 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 32 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 = 0.4122 r_free = 0.4122 target = 0.140384 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.124326 restraints weight = 17554.114| |-----------------------------------------------------------------------------| r_work (start): 0.3906 rms_B_bonded: 1.65 r_work: 0.3852 rms_B_bonded: 1.77 restraints_weight: 0.5000 r_work: 0.3768 rms_B_bonded: 3.11 restraints_weight: 0.2500 r_work (final): 0.3768 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 moved from start: 0.3413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 4347 Z= 0.278 Angle : 0.691 4.316 5929 Z= 0.371 Chirality : 0.046 0.148 693 Planarity : 0.003 0.024 749 Dihedral : 6.521 17.343 616 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 4.11 % Allowed : 13.42 % Favored : 82.47 % 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: -4.91 (0.19), residues: 567 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.73 (0.15), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP F 92 PHE 0.013 0.003 PHE E 101 TYR 0.013 0.001 TYR E 37 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1134 Ramachandran restraints generated. 567 Oldfield, 0 Emsley, 567 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1134 Ramachandran restraints generated. 567 Oldfield, 0 Emsley, 567 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 160 time to evaluate : 0.621 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 84 GLU cc_start: 0.6998 (OUTLIER) cc_final: 0.6474 (tt0) outliers start: 19 outliers final: 11 residues processed: 165 average time/residue: 0.2493 time to fit residues: 54.6563 Evaluate side-chains 159 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 147 time to evaluate : 0.617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 86 ASP Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 97 LEU Chi-restraints excluded: chain C residue 38 GLN Chi-restraints excluded: chain C residue 84 GLU Chi-restraints excluded: chain C residue 86 ASP Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain B residue 86 ASP Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain A residue 27 SER Chi-restraints excluded: chain A residue 86 ASP Chi-restraints excluded: chain A residue 108 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 6 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 51 optimal weight: 0.4980 chunk 4 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 53 optimal weight: 0.4980 chunk 47 optimal weight: 2.9990 chunk 54 optimal weight: 0.8980 chunk 22 optimal weight: 0.6980 chunk 42 optimal weight: 1.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 32 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 = 0.4061 r_free = 0.4061 target = 0.134676 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.119165 restraints weight = 18168.840| |-----------------------------------------------------------------------------| r_work (start): 0.3859 rms_B_bonded: 1.67 r_work: 0.3801 rms_B_bonded: 1.80 restraints_weight: 0.5000 r_work: 0.3714 rms_B_bonded: 3.14 restraints_weight: 0.2500 r_work (final): 0.3714 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.4352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 4347 Z= 0.249 Angle : 0.663 6.607 5929 Z= 0.346 Chirality : 0.045 0.138 693 Planarity : 0.003 0.022 749 Dihedral : 6.217 15.183 616 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 4.76 % Allowed : 14.50 % Favored : 80.74 % 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: -4.50 (0.22), residues: 567 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.42 (0.17), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP G 92 PHE 0.028 0.006 PHE C 101 TYR 0.017 0.002 TYR B 37 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1134 Ramachandran restraints generated. 567 Oldfield, 0 Emsley, 567 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1134 Ramachandran restraints generated. 567 Oldfield, 0 Emsley, 567 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 149 time to evaluate : 0.705 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 101 PHE cc_start: 0.8121 (m-80) cc_final: 0.7902 (m-80) REVERT: C 84 GLU cc_start: 0.7454 (OUTLIER) cc_final: 0.7217 (tt0) REVERT: C 101 PHE cc_start: 0.8550 (m-80) cc_final: 0.8220 (m-80) REVERT: A 93 GLU cc_start: 0.5002 (pm20) cc_final: 0.4792 (pm20) outliers start: 22 outliers final: 18 residues processed: 154 average time/residue: 0.2802 time to fit residues: 56.2315 Evaluate side-chains 161 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 142 time to evaluate : 0.611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 38 GLN Chi-restraints excluded: chain D residue 86 ASP Chi-restraints excluded: chain E residue 38 GLN Chi-restraints excluded: chain E residue 86 ASP Chi-restraints excluded: chain E residue 97 LEU Chi-restraints excluded: chain C residue 38 GLN Chi-restraints excluded: chain C residue 84 GLU Chi-restraints excluded: chain C residue 86 ASP Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain B residue 27 SER Chi-restraints excluded: chain B residue 38 GLN Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 86 ASP Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain A residue 27 SER Chi-restraints excluded: chain A residue 38 GLN Chi-restraints excluded: chain A residue 86 ASP Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain G residue 38 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 42 optimal weight: 1.9990 chunk 44 optimal weight: 0.0970 chunk 47 optimal weight: 0.0670 chunk 9 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 chunk 7 optimal weight: 2.9990 chunk 4 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 19 optimal weight: 0.9980 chunk 27 optimal weight: 0.6980 chunk 48 optimal weight: 2.9990 overall best weight: 0.7718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 32 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 = 0.4052 r_free = 0.4052 target = 0.130276 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.114274 restraints weight = 17894.435| |-----------------------------------------------------------------------------| r_work (start): 0.3834 rms_B_bonded: 1.73 r_work: 0.3765 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.3675 rms_B_bonded: 3.36 restraints_weight: 0.2500 r_work (final): 0.3675 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.4847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 4347 Z= 0.205 Angle : 0.603 4.311 5929 Z= 0.317 Chirality : 0.044 0.139 693 Planarity : 0.003 0.025 749 Dihedral : 6.085 16.647 616 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 3.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 4.55 % Allowed : 16.23 % Favored : 79.22 % 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: -4.30 (0.23), residues: 567 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.27 (0.18), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP G 92 PHE 0.014 0.003 PHE D 101 TYR 0.012 0.001 TYR B 37 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1134 Ramachandran restraints generated. 567 Oldfield, 0 Emsley, 567 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1134 Ramachandran restraints generated. 567 Oldfield, 0 Emsley, 567 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 139 time to evaluate : 0.737 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 46 LYS cc_start: 0.8484 (ttmt) cc_final: 0.8274 (ttmt) REVERT: C 84 GLU cc_start: 0.7541 (OUTLIER) cc_final: 0.6757 (tt0) REVERT: B 84 GLU cc_start: 0.7216 (mt-10) cc_final: 0.6899 (tt0) outliers start: 21 outliers final: 16 residues processed: 144 average time/residue: 0.2813 time to fit residues: 53.0136 Evaluate side-chains 151 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 134 time to evaluate : 0.654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 86 ASP Chi-restraints excluded: chain E residue 38 GLN Chi-restraints excluded: chain E residue 86 ASP Chi-restraints excluded: chain E residue 97 LEU Chi-restraints excluded: chain C residue 38 GLN Chi-restraints excluded: chain C residue 84 GLU Chi-restraints excluded: chain C residue 86 ASP Chi-restraints excluded: chain B residue 27 SER Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 86 ASP Chi-restraints excluded: chain B residue 95 SER Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain A residue 27 SER Chi-restraints excluded: chain A residue 38 GLN Chi-restraints excluded: chain A residue 86 ASP Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain G residue 38 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 20 optimal weight: 3.9990 chunk 16 optimal weight: 1.9990 chunk 9 optimal weight: 2.9990 chunk 32 optimal weight: 3.9990 chunk 7 optimal weight: 2.9990 chunk 39 optimal weight: 2.9990 chunk 8 optimal weight: 0.9980 chunk 17 optimal weight: 0.7980 chunk 54 optimal weight: 1.9990 chunk 4 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 32 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 = 0.3978 r_free = 0.3978 target = 0.123603 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.108421 restraints weight = 18324.984| |-----------------------------------------------------------------------------| r_work (start): 0.3759 rms_B_bonded: 1.76 r_work: 0.3692 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.3603 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.3603 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 moved from start: 0.5487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 4347 Z= 0.381 Angle : 0.663 4.833 5929 Z= 0.352 Chirality : 0.045 0.140 693 Planarity : 0.003 0.026 749 Dihedral : 6.140 16.803 616 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 3.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.35 % Favored : 93.65 % Rotamer: Outliers : 6.28 % Allowed : 16.67 % Favored : 77.06 % 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: -4.24 (0.24), residues: 567 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.22 (0.18), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP G 92 PHE 0.022 0.004 PHE E 101 TYR 0.017 0.002 TYR B 37 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1134 Ramachandran restraints generated. 567 Oldfield, 0 Emsley, 567 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1134 Ramachandran restraints generated. 567 Oldfield, 0 Emsley, 567 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 135 time to evaluate : 1.142 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 84 GLU cc_start: 0.7673 (OUTLIER) cc_final: 0.6839 (tt0) REVERT: B 84 GLU cc_start: 0.7396 (mt-10) cc_final: 0.7139 (mt-10) outliers start: 29 outliers final: 19 residues processed: 146 average time/residue: 0.3722 time to fit residues: 74.7436 Evaluate side-chains 151 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 131 time to evaluate : 0.696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 38 GLN Chi-restraints excluded: chain D residue 86 ASP Chi-restraints excluded: chain D residue 108 THR Chi-restraints excluded: chain E residue 38 GLN Chi-restraints excluded: chain E residue 86 ASP Chi-restraints excluded: chain E residue 97 LEU Chi-restraints excluded: chain C residue 38 GLN Chi-restraints excluded: chain C residue 84 GLU Chi-restraints excluded: chain C residue 86 ASP Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain B residue 38 GLN Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 86 ASP Chi-restraints excluded: chain B residue 95 SER Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain A residue 86 ASP Chi-restraints excluded: chain A residue 91 THR Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain G residue 38 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 6 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 chunk 19 optimal weight: 0.7980 chunk 37 optimal weight: 0.9990 chunk 30 optimal weight: 0.5980 chunk 49 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 46 optimal weight: 0.6980 chunk 1 optimal weight: 0.6980 chunk 22 optimal weight: 1.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 38 GLN E 38 GLN F 38 GLN ** C 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 38 GLN ** B 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 38 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.125814 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.110370 restraints weight = 18234.016| |-----------------------------------------------------------------------------| r_work (start): 0.3781 rms_B_bonded: 1.78 r_work: 0.3710 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.3619 rms_B_bonded: 3.43 restraints_weight: 0.2500 r_work (final): 0.3619 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.5802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 4347 Z= 0.195 Angle : 0.605 5.293 5929 Z= 0.316 Chirality : 0.044 0.141 693 Planarity : 0.003 0.028 749 Dihedral : 5.992 16.482 616 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 4.11 % Allowed : 20.56 % Favored : 75.32 % 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: -4.16 (0.24), residues: 567 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.17 (0.19), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP G 92 PHE 0.024 0.003 PHE F 101 TYR 0.014 0.001 TYR B 37 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1134 Ramachandran restraints generated. 567 Oldfield, 0 Emsley, 567 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1134 Ramachandran restraints generated. 567 Oldfield, 0 Emsley, 567 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 134 time to evaluate : 0.627 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 96 LEU cc_start: 0.8756 (OUTLIER) cc_final: 0.8424 (tp) REVERT: C 84 GLU cc_start: 0.7713 (OUTLIER) cc_final: 0.6860 (tt0) REVERT: B 84 GLU cc_start: 0.7372 (mt-10) cc_final: 0.6981 (tt0) outliers start: 19 outliers final: 15 residues processed: 139 average time/residue: 0.2652 time to fit residues: 48.1596 Evaluate side-chains 148 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 131 time to evaluate : 0.594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 38 GLN Chi-restraints excluded: chain D residue 86 ASP Chi-restraints excluded: chain E residue 38 GLN Chi-restraints excluded: chain E residue 86 ASP Chi-restraints excluded: chain E residue 96 LEU Chi-restraints excluded: chain C residue 38 GLN Chi-restraints excluded: chain C residue 84 GLU Chi-restraints excluded: chain C residue 86 ASP Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 95 SER Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain A residue 86 ASP Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain G residue 38 GLN Chi-restraints excluded: chain G residue 48 LEU Chi-restraints excluded: chain G residue 97 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 53 optimal weight: 0.0570 chunk 18 optimal weight: 2.9990 chunk 4 optimal weight: 2.9990 chunk 44 optimal weight: 2.9990 chunk 41 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 48 optimal weight: 0.6980 chunk 26 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 overall best weight: 1.3504 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 38 GLN ** C 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.123637 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.108590 restraints weight = 18581.380| |-----------------------------------------------------------------------------| r_work (start): 0.3765 rms_B_bonded: 1.76 r_work: 0.3694 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.3604 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.3604 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 moved from start: 0.5934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 4347 Z= 0.316 Angle : 0.649 5.450 5929 Z= 0.345 Chirality : 0.046 0.139 693 Planarity : 0.003 0.027 749 Dihedral : 6.033 16.281 616 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.17 % Favored : 93.83 % Rotamer: Outliers : 3.90 % Allowed : 21.00 % Favored : 75.11 % 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: -4.17 (0.24), residues: 567 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.17 (0.19), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP G 92 PHE 0.010 0.002 PHE E 101 TYR 0.019 0.002 TYR B 37 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1134 Ramachandran restraints generated. 567 Oldfield, 0 Emsley, 567 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1134 Ramachandran restraints generated. 567 Oldfield, 0 Emsley, 567 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 127 time to evaluate : 0.611 Fit side-chains REVERT: E 35 SER cc_start: 0.8886 (t) cc_final: 0.8619 (p) REVERT: E 96 LEU cc_start: 0.8811 (OUTLIER) cc_final: 0.8551 (tp) REVERT: C 84 GLU cc_start: 0.7706 (OUTLIER) cc_final: 0.6872 (tt0) REVERT: B 84 GLU cc_start: 0.7387 (mt-10) cc_final: 0.7139 (mt-10) outliers start: 18 outliers final: 11 residues processed: 130 average time/residue: 0.2728 time to fit residues: 46.1460 Evaluate side-chains 138 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 125 time to evaluate : 0.614 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 86 ASP Chi-restraints excluded: chain E residue 86 ASP Chi-restraints excluded: chain E residue 96 LEU Chi-restraints excluded: chain C residue 84 GLU Chi-restraints excluded: chain C residue 86 ASP Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 86 ASP Chi-restraints excluded: chain B residue 95 SER Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain A residue 86 ASP Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain G residue 97 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 30 optimal weight: 2.9990 chunk 53 optimal weight: 0.2980 chunk 25 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 33 optimal weight: 0.9980 chunk 1 optimal weight: 0.7980 chunk 12 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 32 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 = 0.3981 r_free = 0.3981 target = 0.123716 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.108606 restraints weight = 18689.472| |-----------------------------------------------------------------------------| r_work (start): 0.3765 rms_B_bonded: 1.76 r_work: 0.3695 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.3603 rms_B_bonded: 3.42 restraints_weight: 0.2500 r_work (final): 0.3603 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 moved from start: 0.6118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 4347 Z= 0.288 Angle : 0.626 4.337 5929 Z= 0.331 Chirality : 0.044 0.141 693 Planarity : 0.003 0.028 749 Dihedral : 5.988 17.214 616 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 3.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 3.46 % Allowed : 21.43 % Favored : 75.11 % 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: -4.16 (0.24), residues: 567 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.16 (0.19), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP D 36 PHE 0.009 0.002 PHE E 101 TYR 0.017 0.002 TYR B 37 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1134 Ramachandran restraints generated. 567 Oldfield, 0 Emsley, 567 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1134 Ramachandran restraints generated. 567 Oldfield, 0 Emsley, 567 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 122 time to evaluate : 0.625 Fit side-chains revert: symmetry clash REVERT: E 96 LEU cc_start: 0.8767 (OUTLIER) cc_final: 0.8542 (tp) REVERT: C 84 GLU cc_start: 0.7751 (OUTLIER) cc_final: 0.6945 (tt0) REVERT: C 96 LEU cc_start: 0.8719 (tp) cc_final: 0.8415 (tp) outliers start: 16 outliers final: 14 residues processed: 124 average time/residue: 0.3210 time to fit residues: 52.1739 Evaluate side-chains 133 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 117 time to evaluate : 1.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 86 ASP Chi-restraints excluded: chain E residue 86 ASP Chi-restraints excluded: chain E residue 96 LEU Chi-restraints excluded: chain C residue 84 GLU Chi-restraints excluded: chain C residue 86 ASP Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 86 ASP Chi-restraints excluded: chain B residue 95 SER Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain A residue 86 ASP Chi-restraints excluded: chain A residue 93 GLU Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain G residue 28 ASN Chi-restraints excluded: chain G residue 97 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 44 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 16 optimal weight: 0.9990 chunk 53 optimal weight: 0.0050 chunk 29 optimal weight: 1.9990 chunk 54 optimal weight: 0.0030 chunk 21 optimal weight: 0.9980 chunk 0 optimal weight: 2.9990 chunk 55 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 overall best weight: 0.8008 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 32 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 = 0.3990 r_free = 0.3990 target = 0.124281 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.109145 restraints weight = 18802.991| |-----------------------------------------------------------------------------| r_work (start): 0.3773 rms_B_bonded: 1.79 r_work: 0.3703 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.3612 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.3612 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8239 moved from start: 0.6243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 4347 Z= 0.216 Angle : 0.591 4.221 5929 Z= 0.312 Chirality : 0.044 0.140 693 Planarity : 0.003 0.027 749 Dihedral : 5.880 16.996 616 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 3.03 % Allowed : 21.21 % Favored : 75.76 % 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: -4.15 (0.25), residues: 567 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.16 (0.19), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP G 92 PHE 0.007 0.001 PHE E 101 TYR 0.015 0.001 TYR B 37 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1134 Ramachandran restraints generated. 567 Oldfield, 0 Emsley, 567 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1134 Ramachandran restraints generated. 567 Oldfield, 0 Emsley, 567 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 119 time to evaluate : 0.627 Fit side-chains revert: symmetry clash REVERT: E 96 LEU cc_start: 0.8740 (OUTLIER) cc_final: 0.8525 (tp) REVERT: C 84 GLU cc_start: 0.7757 (OUTLIER) cc_final: 0.6969 (tt0) outliers start: 14 outliers final: 12 residues processed: 120 average time/residue: 0.3026 time to fit residues: 46.9994 Evaluate side-chains 133 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 119 time to evaluate : 0.729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 86 ASP Chi-restraints excluded: chain E residue 86 ASP Chi-restraints excluded: chain E residue 96 LEU Chi-restraints excluded: chain C residue 84 GLU Chi-restraints excluded: chain C residue 86 ASP Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain B residue 86 ASP Chi-restraints excluded: chain B residue 95 SER Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain A residue 86 ASP Chi-restraints excluded: chain A residue 93 GLU Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain G residue 28 ASN Chi-restraints excluded: chain G residue 97 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 25 optimal weight: 2.9990 chunk 41 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 4 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 16 optimal weight: 0.9980 chunk 0 optimal weight: 2.9990 chunk 14 optimal weight: 0.5980 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 32 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 = 0.3950 r_free = 0.3950 target = 0.121263 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.106659 restraints weight = 18828.012| |-----------------------------------------------------------------------------| r_work (start): 0.3742 rms_B_bonded: 1.75 r_work: 0.3673 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.3582 rms_B_bonded: 3.38 restraints_weight: 0.2500 r_work (final): 0.3582 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 moved from start: 0.6420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.040 4347 Z= 0.367 Angle : 0.641 4.421 5929 Z= 0.341 Chirality : 0.045 0.141 693 Planarity : 0.003 0.029 749 Dihedral : 6.013 17.138 616 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.70 % Favored : 93.30 % Rotamer: Outliers : 3.46 % Allowed : 20.35 % Favored : 76.19 % 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: -4.22 (0.24), residues: 567 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.21 (0.18), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 36 PHE 0.007 0.001 PHE G 101 TYR 0.016 0.002 TYR B 37 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1134 Ramachandran restraints generated. 567 Oldfield, 0 Emsley, 567 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1134 Ramachandran restraints generated. 567 Oldfield, 0 Emsley, 567 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 119 time to evaluate : 0.662 Fit side-chains REVERT: E 96 LEU cc_start: 0.8910 (OUTLIER) cc_final: 0.8706 (tp) REVERT: F 93 GLU cc_start: 0.8498 (mt-10) cc_final: 0.8297 (mt-10) REVERT: C 84 GLU cc_start: 0.7788 (OUTLIER) cc_final: 0.6897 (tt0) REVERT: A 93 GLU cc_start: 0.6050 (OUTLIER) cc_final: 0.4841 (pt0) outliers start: 16 outliers final: 11 residues processed: 122 average time/residue: 0.2911 time to fit residues: 46.3744 Evaluate side-chains 130 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 116 time to evaluate : 0.707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 86 ASP Chi-restraints excluded: chain E residue 86 ASP Chi-restraints excluded: chain E residue 96 LEU Chi-restraints excluded: chain C residue 84 GLU Chi-restraints excluded: chain C residue 86 ASP Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain B residue 86 ASP Chi-restraints excluded: chain B residue 95 SER Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain A residue 86 ASP Chi-restraints excluded: chain A residue 93 GLU Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain G residue 97 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 51 optimal weight: 0.6980 chunk 49 optimal weight: 1.9990 chunk 24 optimal weight: 3.9990 chunk 21 optimal weight: 0.9990 chunk 35 optimal weight: 0.9990 chunk 19 optimal weight: 0.5980 chunk 2 optimal weight: 1.9990 chunk 4 optimal weight: 2.9990 chunk 5 optimal weight: 3.9990 chunk 10 optimal weight: 0.5980 chunk 32 optimal weight: 0.7980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 32 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 = 0.3985 r_free = 0.3985 target = 0.123457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.108651 restraints weight = 18848.127| |-----------------------------------------------------------------------------| r_work (start): 0.3768 rms_B_bonded: 1.77 r_work: 0.3701 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.3610 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.3610 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.6477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 4347 Z= 0.206 Angle : 0.592 4.185 5929 Z= 0.313 Chirality : 0.044 0.140 693 Planarity : 0.003 0.028 749 Dihedral : 5.873 17.920 616 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 3.03 % Allowed : 21.43 % Favored : 75.54 % 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: -4.16 (0.24), residues: 567 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.17 (0.19), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 36 PHE 0.009 0.002 PHE E 101 TYR 0.018 0.002 TYR B 37 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5272.53 seconds wall clock time: 90 minutes 57.75 seconds (5457.75 seconds total)