Starting phenix.real_space_refine on Thu Mar 6 01:09:03 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bpu_44790/03_2025/9bpu_44790.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bpu_44790/03_2025/9bpu_44790.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.26 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9bpu_44790/03_2025/9bpu_44790.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bpu_44790/03_2025/9bpu_44790.map" model { file = "/net/cci-nas-00/data/ceres_data/9bpu_44790/03_2025/9bpu_44790.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bpu_44790/03_2025/9bpu_44790.cif" } resolution = 3.26 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 27 5.16 5 C 2744 2.51 5 N 743 2.21 5 O 804 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 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: 4318 Number of models: 1 Model: "" Number of chains: 5 Chain: "C" Number of atoms: 1068 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1068 Classifications: {'peptide': 138} Link IDs: {'PTRANS': 10, 'TRANS': 127} Chain breaks: 1 Chain: "A" Number of atoms: 1613 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1613 Classifications: {'peptide': 195} Link IDs: {'PTRANS': 12, 'TRANS': 182} Chain: "B" Number of atoms: 1570 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1570 Classifications: {'peptide': 196} Link IDs: {'PTRANS': 19, 'TRANS': 176} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 3.06, per 1000 atoms: 0.71 Number of scatterers: 4318 At special positions: 0 Unit cell: (67.284, 96.12, 104.664, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 27 16.00 O 804 8.00 N 743 7.00 C 2744 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS C 27 " - pdb=" SG CYS C 122 " distance=2.03 Simple disulfide: pdb=" SG CYS C 62 " - pdb=" SG CYS C 152 " distance=2.03 Simple disulfide: pdb=" SG CYS C 76 " - pdb=" SG CYS C 178 " distance=2.03 Simple disulfide: pdb=" SG CYS A 66 " - pdb=" SG CYS A 74 " distance=2.03 Simple disulfide: pdb=" SG CYS A 188 " - pdb=" SG CYS A 209 " distance=2.03 Simple disulfide: pdb=" SG CYS B 54 " - pdb=" SG CYS B 62 " distance=2.02 Simple disulfide: pdb=" SG CYS B 175 " - pdb=" SG CYS B 197 " distance=2.03 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 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " NAG-ASN " NAG D 1 " - " ASN B 9 " " NAG E 1 " - " ASN B 122 " Time building additional restraints: 1.18 Conformation dependent library (CDL) restraints added in 466.8 milliseconds 1042 Ramachandran restraints generated. 521 Oldfield, 0 Emsley, 521 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1016 Finding SS restraints... Secondary structure from input PDB file: 9 helices and 12 sheets defined 23.4% alpha, 41.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.51 Creating SS restraints... Processing helix chain 'C' and resid 28 through 33 removed outlier: 4.146A pdb=" N HIS C 31 " --> pdb=" O LEU C 28 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ARG C 33 " --> pdb=" O SER C 30 " (cutoff:3.500A) Processing helix chain 'C' and resid 36 through 58 Processing helix chain 'C' and resid 74 through 99 removed outlier: 3.565A pdb=" N SER C 99 " --> pdb=" O GLY C 95 " (cutoff:3.500A) Processing helix chain 'C' and resid 105 through 127 Processing helix chain 'C' and resid 149 through 167 removed outlier: 3.690A pdb=" N ARG C 153 " --> pdb=" O SER C 149 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N LEU C 162 " --> pdb=" O VAL C 158 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N ARG C 163 " --> pdb=" O PHE C 159 " (cutoff:3.500A) Processing helix chain 'C' and resid 167 through 176 Processing helix chain 'A' and resid 106 through 111 Processing helix chain 'A' and resid 144 through 149 Processing helix chain 'B' and resid 99 through 103 Processing sheet with id=AA1, first strand: chain 'A' and resid 25 through 32 removed outlier: 4.297A pdb=" N VAL A 27 " --> pdb=" O GLN A 39 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N GLN A 39 " --> pdb=" O VAL A 27 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N MET A 29 " --> pdb=" O ILE A 37 " (cutoff:3.500A) removed outlier: 5.977A pdb=" N ILE A 37 " --> pdb=" O MET A 29 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N SER A 31 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 5.330A pdb=" N LYS A 35 " --> pdb=" O SER A 31 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 61 through 69 removed outlier: 6.715A pdb=" N ALA A 54 " --> pdb=" O LYS A 65 " (cutoff:3.500A) removed outlier: 4.795A pdb=" N MET A 67 " --> pdb=" O PHE A 52 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N PHE A 52 " --> pdb=" O MET A 67 " (cutoff:3.500A) removed outlier: 4.874A pdb=" N THR A 86 " --> pdb=" O LEU A 57 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 61 through 69 removed outlier: 6.715A pdb=" N ALA A 54 " --> pdb=" O LYS A 65 " (cutoff:3.500A) removed outlier: 4.795A pdb=" N MET A 67 " --> pdb=" O PHE A 52 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N PHE A 52 " --> pdb=" O MET A 67 " (cutoff:3.500A) removed outlier: 4.874A pdb=" N THR A 86 " --> pdb=" O LEU A 57 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 117 through 123 Processing sheet with id=AA5, first strand: chain 'A' and resid 167 through 169 Processing sheet with id=AA6, first strand: chain 'A' and resid 167 through 169 Processing sheet with id=AA7, first strand: chain 'B' and resid 11 through 15 Processing sheet with id=AA8, first strand: chain 'B' and resid 34 through 41 Processing sheet with id=AA9, first strand: chain 'B' and resid 34 through 41 Processing sheet with id=AB1, first strand: chain 'B' and resid 109 through 114 removed outlier: 3.594A pdb=" N ASN B 122 " --> pdb=" O VAL B 111 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 151 through 152 Processing sheet with id=AB3, first strand: chain 'B' and resid 151 through 152 222 hydrogen bonds defined for protein. 576 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: 1.26 Time building geometry restraints manager: 1.35 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1328 1.34 - 1.45: 732 1.45 - 1.57: 2336 1.57 - 1.69: 1 1.69 - 1.81: 37 Bond restraints: 4434 Sorted by residual: bond pdb=" N MET B 131 " pdb=" CA MET B 131 " ideal model delta sigma weight residual 1.453 1.489 -0.035 9.20e-03 1.18e+04 1.48e+01 bond pdb=" N TYR B 39 " pdb=" CA TYR B 39 " ideal model delta sigma weight residual 1.454 1.491 -0.037 1.23e-02 6.61e+03 8.83e+00 bond pdb=" N SER B 190 " pdb=" CA SER B 190 " ideal model delta sigma weight residual 1.455 1.487 -0.032 1.09e-02 8.42e+03 8.60e+00 bond pdb=" N VAL A 122 " pdb=" CA VAL A 122 " ideal model delta sigma weight residual 1.459 1.493 -0.034 1.20e-02 6.94e+03 8.14e+00 bond pdb=" N TYR B 125 " pdb=" CA TYR B 125 " ideal model delta sigma weight residual 1.454 1.489 -0.035 1.23e-02 6.61e+03 7.99e+00 ... (remaining 4429 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.73: 5733 1.73 - 3.45: 251 3.45 - 5.18: 39 5.18 - 6.90: 7 6.90 - 8.63: 2 Bond angle restraints: 6032 Sorted by residual: angle pdb=" C ALA A 124 " pdb=" CA ALA A 124 " pdb=" CB ALA A 124 " ideal model delta sigma weight residual 117.23 111.85 5.38 1.36e+00 5.41e-01 1.57e+01 angle pdb=" CA GLN B 126 " pdb=" C GLN B 126 " pdb=" O GLN B 126 " ideal model delta sigma weight residual 122.51 118.14 4.37 1.34e+00 5.57e-01 1.06e+01 angle pdb=" CA ASP B 71 " pdb=" C ASP B 71 " pdb=" O ASP B 71 " ideal model delta sigma weight residual 121.58 118.05 3.53 1.12e+00 7.97e-01 9.95e+00 angle pdb=" CA GLN B 8 " pdb=" C GLN B 8 " pdb=" O GLN B 8 " ideal model delta sigma weight residual 120.70 117.54 3.16 1.03e+00 9.43e-01 9.43e+00 angle pdb=" CA GLY A 48 " pdb=" C GLY A 48 " pdb=" O GLY A 48 " ideal model delta sigma weight residual 122.33 118.28 4.05 1.32e+00 5.74e-01 9.42e+00 ... (remaining 6027 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.12: 2479 22.12 - 44.25: 233 44.25 - 66.37: 45 66.37 - 88.49: 9 88.49 - 110.62: 6 Dihedral angle restraints: 2772 sinusoidal: 1210 harmonic: 1562 Sorted by residual: dihedral pdb=" CB CYS C 62 " pdb=" SG CYS C 62 " pdb=" SG CYS C 152 " pdb=" CB CYS C 152 " ideal model delta sinusoidal sigma weight residual 93.00 61.02 31.98 1 1.00e+01 1.00e-02 1.46e+01 dihedral pdb=" O4 BMA E 3 " pdb=" C4 BMA E 3 " pdb=" C5 BMA E 3 " pdb=" O5 BMA E 3 " ideal model delta sinusoidal sigma weight residual 288.71 178.09 110.62 1 3.00e+01 1.11e-03 1.44e+01 dihedral pdb=" C3 BMA E 3 " pdb=" C4 BMA E 3 " pdb=" C5 BMA E 3 " pdb=" O5 BMA E 3 " ideal model delta sinusoidal sigma weight residual 47.62 -61.13 108.75 1 3.00e+01 1.11e-03 1.41e+01 ... (remaining 2769 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 530 0.054 - 0.107: 101 0.107 - 0.161: 31 0.161 - 0.214: 5 0.214 - 0.268: 2 Chirality restraints: 669 Sorted by residual: chirality pdb=" C5 BMA E 3 " pdb=" C4 BMA E 3 " pdb=" C6 BMA E 3 " pdb=" O5 BMA E 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.54 0.27 2.00e-01 2.50e+01 1.79e+00 chirality pdb=" C1 NAG E 1 " pdb=" ND2 ASN B 122 " pdb=" C2 NAG E 1 " pdb=" O5 NAG E 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.18 -0.22 2.00e-01 2.50e+01 1.26e+00 chirality pdb=" C1 NAG D 1 " pdb=" ND2 ASN B 9 " pdb=" C2 NAG D 1 " pdb=" O5 NAG D 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.20 -0.20 2.00e-01 2.50e+01 9.52e-01 ... (remaining 666 not shown) Planarity restraints: 775 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER A 42 " 0.035 5.00e-02 4.00e+02 5.13e-02 4.21e+00 pdb=" N PRO A 43 " -0.089 5.00e-02 4.00e+02 pdb=" CA PRO A 43 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 43 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CG GLU B 50 " -0.009 2.00e-02 2.50e+03 1.78e-02 3.17e+00 pdb=" CD GLU B 50 " 0.031 2.00e-02 2.50e+03 pdb=" OE1 GLU B 50 " -0.011 2.00e-02 2.50e+03 pdb=" OE2 GLU B 50 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 100 " -0.016 2.00e-02 2.50e+03 8.96e-03 2.01e+00 pdb=" CG TRP A 100 " 0.022 2.00e-02 2.50e+03 pdb=" CD1 TRP A 100 " -0.001 2.00e-02 2.50e+03 pdb=" CD2 TRP A 100 " -0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP A 100 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP A 100 " -0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP A 100 " 0.006 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 100 " -0.006 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 100 " -0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP A 100 " -0.000 2.00e-02 2.50e+03 ... (remaining 772 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 523 2.75 - 3.29: 4033 3.29 - 3.83: 7185 3.83 - 4.36: 8209 4.36 - 4.90: 14499 Nonbonded interactions: 34449 Sorted by model distance: nonbonded pdb=" OH TYR B 138 " pdb=" O GLN B 160 " model vdw 2.216 3.040 nonbonded pdb=" OG SER B 84 " pdb=" O SER B 87 " model vdw 2.235 3.040 nonbonded pdb=" OG1 THR A 53 " pdb=" OE1 GLU A 92 " model vdw 2.248 3.040 nonbonded pdb=" NE2 GLN A 157 " pdb=" OE1 GLN A 190 " model vdw 2.296 3.120 nonbonded pdb=" NH2 ARG C 47 " pdb=" OD2 ASP B 98 " model vdw 2.336 3.120 ... (remaining 34444 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=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: 0.690 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.170 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 14.350 Find NCS groups from input model: 0.050 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:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7519 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 : 0.006 0.087 4434 Z= 0.352 Angle : 0.779 8.626 6032 Z= 0.455 Chirality : 0.051 0.268 669 Planarity : 0.004 0.051 773 Dihedral : 17.752 110.615 1735 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 0.64 % Allowed : 24.79 % Favored : 74.57 % 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: -0.01 (0.38), residues: 521 helix: 1.86 (0.49), residues: 119 sheet: -0.54 (0.36), residues: 203 loop : -0.42 (0.45), residues: 199 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 100 HIS 0.007 0.001 HIS A 97 PHE 0.007 0.001 PHE B 153 TYR 0.012 0.001 TYR B 125 ARG 0.005 0.000 ARG A 88 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1042 Ramachandran restraints generated. 521 Oldfield, 0 Emsley, 521 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1042 Ramachandran restraints generated. 521 Oldfield, 0 Emsley, 521 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 96 time to evaluate : 0.477 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 127 LEU cc_start: 0.8178 (mt) cc_final: 0.7926 (mt) outliers start: 3 outliers final: 2 residues processed: 98 average time/residue: 0.1712 time to fit residues: 21.0104 Evaluate side-chains 88 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 86 time to evaluate : 0.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain B residue 134 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 43 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 chunk 26 optimal weight: 0.9990 chunk 20 optimal weight: 0.8980 chunk 39 optimal weight: 0.7980 chunk 15 optimal weight: 0.0170 chunk 24 optimal weight: 1.9990 chunk 29 optimal weight: 3.9990 chunk 46 optimal weight: 3.9990 overall best weight: 0.9422 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 168 GLN B 167 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.175722 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.147269 restraints weight = 5379.707| |-----------------------------------------------------------------------------| r_work (start): 0.3765 rms_B_bonded: 2.40 r_work: 0.3648 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3490 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3490 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7620 moved from start: 0.0955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 4434 Z= 0.225 Angle : 0.603 7.111 6032 Z= 0.296 Chirality : 0.042 0.136 669 Planarity : 0.004 0.034 773 Dihedral : 9.331 63.099 690 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 4.70 % Allowed : 21.58 % Favored : 73.72 % 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: 0.11 (0.37), residues: 521 helix: 1.86 (0.49), residues: 119 sheet: -0.47 (0.36), residues: 202 loop : -0.27 (0.44), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 100 HIS 0.004 0.001 HIS A 97 PHE 0.018 0.001 PHE A 62 TYR 0.015 0.001 TYR B 138 ARG 0.004 0.000 ARG A 88 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1042 Ramachandran restraints generated. 521 Oldfield, 0 Emsley, 521 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1042 Ramachandran restraints generated. 521 Oldfield, 0 Emsley, 521 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 85 time to evaluate : 0.640 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 26 ASN cc_start: 0.8443 (t0) cc_final: 0.8191 (t0) REVERT: A 88 ARG cc_start: 0.8535 (ttp80) cc_final: 0.8196 (ttp-170) REVERT: B 40 GLN cc_start: 0.7906 (OUTLIER) cc_final: 0.7409 (tt0) REVERT: B 117 GLU cc_start: 0.7295 (pt0) cc_final: 0.7091 (pt0) outliers start: 22 outliers final: 12 residues processed: 97 average time/residue: 0.2115 time to fit residues: 26.5402 Evaluate side-chains 88 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 75 time to evaluate : 0.681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 112 LEU Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain B residue 24 LEU Chi-restraints excluded: chain B residue 40 GLN Chi-restraints excluded: chain B residue 88 LYS Chi-restraints excluded: chain B residue 113 THR Chi-restraints excluded: chain B residue 131 MET Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 185 SER Chi-restraints excluded: chain B residue 199 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 16 optimal weight: 5.9990 chunk 7 optimal weight: 1.9990 chunk 14 optimal weight: 0.5980 chunk 38 optimal weight: 0.7980 chunk 24 optimal weight: 2.9990 chunk 32 optimal weight: 0.7980 chunk 13 optimal weight: 3.9990 chunk 31 optimal weight: 0.5980 chunk 12 optimal weight: 0.8980 chunk 0 optimal weight: 7.9990 chunk 36 optimal weight: 6.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 167 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4085 r_free = 0.4085 target = 0.175382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.147141 restraints weight = 5335.145| |-----------------------------------------------------------------------------| r_work (start): 0.3771 rms_B_bonded: 2.39 r_work: 0.3650 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3499 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3499 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7613 moved from start: 0.1199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4434 Z= 0.192 Angle : 0.573 7.164 6032 Z= 0.278 Chirality : 0.041 0.133 669 Planarity : 0.004 0.030 773 Dihedral : 7.786 55.908 690 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 4.27 % Allowed : 21.15 % Favored : 74.57 % 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: 0.33 (0.38), residues: 521 helix: 2.53 (0.48), residues: 111 sheet: -0.42 (0.36), residues: 201 loop : -0.25 (0.44), residues: 209 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 100 HIS 0.004 0.001 HIS A 97 PHE 0.010 0.001 PHE A 62 TYR 0.011 0.001 TYR B 138 ARG 0.002 0.000 ARG A 60 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1042 Ramachandran restraints generated. 521 Oldfield, 0 Emsley, 521 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1042 Ramachandran restraints generated. 521 Oldfield, 0 Emsley, 521 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 76 time to evaluate : 1.288 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 26 ASN cc_start: 0.8469 (t0) cc_final: 0.7967 (t0) REVERT: A 88 ARG cc_start: 0.8458 (ttp-170) cc_final: 0.8005 (ttp-170) REVERT: B 40 GLN cc_start: 0.7833 (OUTLIER) cc_final: 0.7344 (tt0) REVERT: B 117 GLU cc_start: 0.7202 (pt0) cc_final: 0.6856 (pt0) outliers start: 20 outliers final: 14 residues processed: 89 average time/residue: 0.2642 time to fit residues: 30.5329 Evaluate side-chains 94 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 79 time to evaluate : 0.674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 57 TRP Chi-restraints excluded: chain C residue 112 LEU Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain B residue 18 SER Chi-restraints excluded: chain B residue 24 LEU Chi-restraints excluded: chain B residue 40 GLN Chi-restraints excluded: chain B residue 61 LEU Chi-restraints excluded: chain B residue 113 THR Chi-restraints excluded: chain B residue 131 MET Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 191 LYS Chi-restraints excluded: chain B residue 199 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 32 optimal weight: 1.9990 chunk 35 optimal weight: 3.9990 chunk 12 optimal weight: 2.9990 chunk 10 optimal weight: 9.9990 chunk 17 optimal weight: 5.9990 chunk 14 optimal weight: 0.6980 chunk 20 optimal weight: 4.9990 chunk 27 optimal weight: 4.9990 chunk 25 optimal weight: 3.9990 chunk 11 optimal weight: 1.9990 chunk 8 optimal weight: 0.8980 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 70 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.169740 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.140852 restraints weight = 5423.767| |-----------------------------------------------------------------------------| r_work (start): 0.3695 rms_B_bonded: 2.43 r_work: 0.3571 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3406 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3406 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7686 moved from start: 0.1565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.036 4434 Z= 0.367 Angle : 0.655 6.869 6032 Z= 0.323 Chirality : 0.043 0.138 669 Planarity : 0.004 0.032 773 Dihedral : 7.415 56.424 690 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 5.56 % Allowed : 18.38 % Favored : 76.07 % 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: -0.01 (0.37), residues: 521 helix: 2.16 (0.47), residues: 111 sheet: -0.67 (0.36), residues: 201 loop : -0.35 (0.44), residues: 209 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 152 HIS 0.005 0.001 HIS A 97 PHE 0.014 0.002 PHE A 62 TYR 0.016 0.002 TYR B 99 ARG 0.003 0.001 ARG C 33 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1042 Ramachandran restraints generated. 521 Oldfield, 0 Emsley, 521 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1042 Ramachandran restraints generated. 521 Oldfield, 0 Emsley, 521 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 85 time to evaluate : 1.216 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 ASN cc_start: 0.8540 (t0) cc_final: 0.7976 (t0) REVERT: B 40 GLN cc_start: 0.8174 (OUTLIER) cc_final: 0.7576 (tt0) REVERT: B 59 GLU cc_start: 0.6843 (mt-10) cc_final: 0.6353 (pt0) REVERT: B 117 GLU cc_start: 0.7210 (pt0) cc_final: 0.6731 (pt0) outliers start: 26 outliers final: 19 residues processed: 104 average time/residue: 0.2889 time to fit residues: 38.9818 Evaluate side-chains 109 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 89 time to evaluate : 0.505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 57 TRP Chi-restraints excluded: chain C residue 102 LEU Chi-restraints excluded: chain C residue 112 LEU Chi-restraints excluded: chain C residue 122 CYS Chi-restraints excluded: chain C residue 149 SER Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain B residue 14 SER Chi-restraints excluded: chain B residue 18 SER Chi-restraints excluded: chain B residue 24 LEU Chi-restraints excluded: chain B residue 40 GLN Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 88 LYS Chi-restraints excluded: chain B residue 113 THR Chi-restraints excluded: chain B residue 131 MET Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 185 SER Chi-restraints excluded: chain B residue 199 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 40 optimal weight: 0.8980 chunk 41 optimal weight: 0.9990 chunk 16 optimal weight: 5.9990 chunk 24 optimal weight: 0.7980 chunk 19 optimal weight: 0.9990 chunk 14 optimal weight: 0.6980 chunk 12 optimal weight: 1.9990 chunk 33 optimal weight: 0.6980 chunk 35 optimal weight: 3.9990 chunk 30 optimal weight: 0.7980 chunk 8 optimal weight: 2.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.173374 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.144598 restraints weight = 5464.927| |-----------------------------------------------------------------------------| r_work (start): 0.3747 rms_B_bonded: 2.44 r_work: 0.3624 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work (final): 0.3624 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7509 moved from start: 0.1604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4434 Z= 0.197 Angle : 0.582 7.591 6032 Z= 0.285 Chirality : 0.041 0.137 669 Planarity : 0.004 0.031 773 Dihedral : 7.007 55.488 690 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 4.70 % Allowed : 19.23 % Favored : 76.07 % 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: 0.16 (0.38), residues: 521 helix: 2.39 (0.48), residues: 111 sheet: -0.55 (0.37), residues: 201 loop : -0.33 (0.44), residues: 209 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 100 HIS 0.003 0.001 HIS C 31 PHE 0.008 0.001 PHE B 153 TYR 0.011 0.001 TYR B 138 ARG 0.003 0.000 ARG A 60 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1042 Ramachandran restraints generated. 521 Oldfield, 0 Emsley, 521 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1042 Ramachandran restraints generated. 521 Oldfield, 0 Emsley, 521 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 86 time to evaluate : 0.495 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 26 ASN cc_start: 0.8332 (t0) cc_final: 0.7851 (t0) REVERT: B 59 GLU cc_start: 0.6532 (mt-10) cc_final: 0.6131 (pt0) REVERT: B 117 GLU cc_start: 0.6991 (pt0) cc_final: 0.6593 (pt0) outliers start: 22 outliers final: 14 residues processed: 101 average time/residue: 0.1502 time to fit residues: 19.3057 Evaluate side-chains 91 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 77 time to evaluate : 0.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 39 THR Chi-restraints excluded: chain C residue 57 TRP Chi-restraints excluded: chain C residue 112 LEU Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain B residue 18 SER Chi-restraints excluded: chain B residue 24 LEU Chi-restraints excluded: chain B residue 40 GLN Chi-restraints excluded: chain B residue 113 THR Chi-restraints excluded: chain B residue 131 MET Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 191 LYS Chi-restraints excluded: chain B residue 199 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 22 optimal weight: 0.9980 chunk 43 optimal weight: 6.9990 chunk 40 optimal weight: 0.9980 chunk 42 optimal weight: 0.5980 chunk 16 optimal weight: 3.9990 chunk 46 optimal weight: 1.9990 chunk 12 optimal weight: 0.7980 chunk 9 optimal weight: 3.9990 chunk 4 optimal weight: 7.9990 chunk 2 optimal weight: 3.9990 chunk 41 optimal weight: 0.0470 overall best weight: 0.6878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.174602 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.145932 restraints weight = 5394.928| |-----------------------------------------------------------------------------| r_work (start): 0.3753 rms_B_bonded: 2.43 r_work: 0.3636 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3473 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3473 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7654 moved from start: 0.1711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 4434 Z= 0.189 Angle : 0.579 7.720 6032 Z= 0.281 Chirality : 0.041 0.145 669 Planarity : 0.004 0.035 773 Dihedral : 6.860 55.087 690 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 5.13 % Allowed : 18.80 % Favored : 76.07 % 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: 0.27 (0.38), residues: 521 helix: 2.48 (0.48), residues: 111 sheet: -0.47 (0.37), residues: 201 loop : -0.26 (0.44), residues: 209 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 100 HIS 0.003 0.001 HIS C 31 PHE 0.007 0.001 PHE B 153 TYR 0.011 0.001 TYR B 138 ARG 0.002 0.000 ARG A 88 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1042 Ramachandran restraints generated. 521 Oldfield, 0 Emsley, 521 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1042 Ramachandran restraints generated. 521 Oldfield, 0 Emsley, 521 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 80 time to evaluate : 0.467 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 26 ASN cc_start: 0.8463 (t0) cc_final: 0.8012 (t0) REVERT: B 59 GLU cc_start: 0.6722 (mt-10) cc_final: 0.6235 (pt0) REVERT: B 68 LYS cc_start: 0.8316 (tppt) cc_final: 0.7967 (tppp) REVERT: B 69 LYS cc_start: 0.8046 (pttt) cc_final: 0.7834 (pttt) REVERT: B 117 GLU cc_start: 0.7261 (pt0) cc_final: 0.6856 (pt0) outliers start: 24 outliers final: 17 residues processed: 97 average time/residue: 0.1678 time to fit residues: 20.5361 Evaluate side-chains 102 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 85 time to evaluate : 0.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 39 THR Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 57 TRP Chi-restraints excluded: chain C residue 112 LEU Chi-restraints excluded: chain C residue 149 SER Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain B residue 18 SER Chi-restraints excluded: chain B residue 24 LEU Chi-restraints excluded: chain B residue 40 GLN Chi-restraints excluded: chain B residue 61 LEU Chi-restraints excluded: chain B residue 88 LYS Chi-restraints excluded: chain B residue 113 THR Chi-restraints excluded: chain B residue 131 MET Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 199 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 49 optimal weight: 1.9990 chunk 4 optimal weight: 9.9990 chunk 29 optimal weight: 3.9990 chunk 45 optimal weight: 0.6980 chunk 34 optimal weight: 7.9990 chunk 6 optimal weight: 0.9990 chunk 16 optimal weight: 1.9990 chunk 26 optimal weight: 0.6980 chunk 15 optimal weight: 1.9990 chunk 31 optimal weight: 0.8980 chunk 39 optimal weight: 2.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.172104 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.143603 restraints weight = 5389.754| |-----------------------------------------------------------------------------| r_work (start): 0.3729 rms_B_bonded: 2.41 r_work: 0.3610 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3444 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3444 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7680 moved from start: 0.1756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 4434 Z= 0.246 Angle : 0.613 7.882 6032 Z= 0.299 Chirality : 0.041 0.141 669 Planarity : 0.004 0.032 773 Dihedral : 6.929 55.417 690 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 4.06 % Allowed : 19.44 % Favored : 76.50 % 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: 0.13 (0.38), residues: 521 helix: 1.94 (0.47), residues: 122 sheet: -0.49 (0.37), residues: 201 loop : -0.29 (0.46), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 100 HIS 0.003 0.001 HIS A 85 PHE 0.009 0.001 PHE B 153 TYR 0.011 0.001 TYR B 138 ARG 0.002 0.000 ARG A 198 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1042 Ramachandran restraints generated. 521 Oldfield, 0 Emsley, 521 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1042 Ramachandran restraints generated. 521 Oldfield, 0 Emsley, 521 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 86 time to evaluate : 0.475 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 ASN cc_start: 0.8482 (t0) cc_final: 0.8023 (t0) REVERT: B 59 GLU cc_start: 0.6761 (mt-10) cc_final: 0.6274 (pt0) REVERT: B 68 LYS cc_start: 0.8310 (tppt) cc_final: 0.7954 (tppp) REVERT: B 117 GLU cc_start: 0.7270 (pt0) cc_final: 0.6848 (pt0) outliers start: 19 outliers final: 18 residues processed: 99 average time/residue: 0.1707 time to fit residues: 21.1966 Evaluate side-chains 100 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 82 time to evaluate : 0.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 39 THR Chi-restraints excluded: chain C residue 57 TRP Chi-restraints excluded: chain C residue 98 ARG Chi-restraints excluded: chain C residue 112 LEU Chi-restraints excluded: chain C residue 149 SER Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain B residue 18 SER Chi-restraints excluded: chain B residue 24 LEU Chi-restraints excluded: chain B residue 40 GLN Chi-restraints excluded: chain B residue 88 LYS Chi-restraints excluded: chain B residue 113 THR Chi-restraints excluded: chain B residue 131 MET Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 191 LYS Chi-restraints excluded: chain B residue 199 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 41 optimal weight: 2.9990 chunk 12 optimal weight: 0.7980 chunk 39 optimal weight: 0.7980 chunk 49 optimal weight: 1.9990 chunk 31 optimal weight: 0.9990 chunk 34 optimal weight: 8.9990 chunk 37 optimal weight: 4.9990 chunk 33 optimal weight: 0.6980 chunk 20 optimal weight: 5.9990 chunk 15 optimal weight: 2.9990 chunk 44 optimal weight: 0.0030 overall best weight: 0.6592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4082 r_free = 0.4082 target = 0.175175 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.146812 restraints weight = 5385.914| |-----------------------------------------------------------------------------| r_work (start): 0.3756 rms_B_bonded: 2.41 r_work: 0.3637 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3472 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3472 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7660 moved from start: 0.1842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 4434 Z= 0.189 Angle : 0.583 7.686 6032 Z= 0.285 Chirality : 0.041 0.148 669 Planarity : 0.004 0.032 773 Dihedral : 6.783 54.878 690 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 3.85 % Allowed : 20.51 % Favored : 75.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.32 (0.38), residues: 521 helix: 2.53 (0.47), residues: 116 sheet: -0.46 (0.37), residues: 194 loop : -0.32 (0.44), residues: 211 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 152 HIS 0.003 0.001 HIS C 31 PHE 0.007 0.001 PHE B 142 TYR 0.010 0.001 TYR B 138 ARG 0.002 0.000 ARG A 90 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1042 Ramachandran restraints generated. 521 Oldfield, 0 Emsley, 521 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1042 Ramachandran restraints generated. 521 Oldfield, 0 Emsley, 521 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 83 time to evaluate : 0.445 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 26 ASN cc_start: 0.8466 (t0) cc_final: 0.8040 (t0) REVERT: B 59 GLU cc_start: 0.6703 (mt-10) cc_final: 0.6216 (pt0) REVERT: B 68 LYS cc_start: 0.8268 (tppt) cc_final: 0.7941 (tppp) REVERT: B 69 LYS cc_start: 0.7873 (pttt) cc_final: 0.7623 (pttt) REVERT: B 117 GLU cc_start: 0.7258 (pt0) cc_final: 0.6825 (pt0) outliers start: 18 outliers final: 17 residues processed: 96 average time/residue: 0.1668 time to fit residues: 20.1498 Evaluate side-chains 99 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 82 time to evaluate : 0.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 39 THR Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 57 TRP Chi-restraints excluded: chain C residue 112 LEU Chi-restraints excluded: chain C residue 149 SER Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain B residue 18 SER Chi-restraints excluded: chain B residue 24 LEU Chi-restraints excluded: chain B residue 40 GLN Chi-restraints excluded: chain B residue 88 LYS Chi-restraints excluded: chain B residue 113 THR Chi-restraints excluded: chain B residue 131 MET Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 191 LYS Chi-restraints excluded: chain B residue 199 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 2 optimal weight: 3.9990 chunk 9 optimal weight: 3.9990 chunk 28 optimal weight: 0.9990 chunk 48 optimal weight: 4.9990 chunk 34 optimal weight: 0.8980 chunk 29 optimal weight: 0.8980 chunk 45 optimal weight: 0.6980 chunk 50 optimal weight: 0.9990 chunk 24 optimal weight: 0.4980 chunk 15 optimal weight: 3.9990 chunk 30 optimal weight: 0.0010 overall best weight: 0.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 70 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.174756 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.146444 restraints weight = 5404.006| |-----------------------------------------------------------------------------| r_work (start): 0.3765 rms_B_bonded: 2.41 r_work: 0.3641 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3480 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3480 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7644 moved from start: 0.1860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 4434 Z= 0.179 Angle : 0.582 7.833 6032 Z= 0.284 Chirality : 0.040 0.150 669 Planarity : 0.004 0.032 773 Dihedral : 6.729 54.758 690 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 3.63 % Allowed : 20.94 % Favored : 75.43 % 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: 0.36 (0.38), residues: 521 helix: 2.56 (0.47), residues: 116 sheet: -0.44 (0.38), residues: 194 loop : -0.28 (0.44), residues: 211 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP A 100 HIS 0.004 0.001 HIS A 97 PHE 0.007 0.001 PHE B 101 TYR 0.010 0.001 TYR B 138 ARG 0.004 0.000 ARG A 60 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1042 Ramachandran restraints generated. 521 Oldfield, 0 Emsley, 521 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1042 Ramachandran restraints generated. 521 Oldfield, 0 Emsley, 521 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 83 time to evaluate : 0.440 Fit side-chains revert: symmetry clash REVERT: A 26 ASN cc_start: 0.8452 (t0) cc_final: 0.8022 (t0) REVERT: A 88 ARG cc_start: 0.8481 (ttp-170) cc_final: 0.7840 (ttp-170) REVERT: B 59 GLU cc_start: 0.6711 (mt-10) cc_final: 0.6230 (pt0) REVERT: B 68 LYS cc_start: 0.8196 (tppt) cc_final: 0.7880 (tppp) REVERT: B 117 GLU cc_start: 0.7255 (pt0) cc_final: 0.6746 (pt0) outliers start: 17 outliers final: 15 residues processed: 93 average time/residue: 0.1743 time to fit residues: 20.3646 Evaluate side-chains 97 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 82 time to evaluate : 0.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 57 TRP Chi-restraints excluded: chain C residue 149 SER Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain B residue 18 SER Chi-restraints excluded: chain B residue 24 LEU Chi-restraints excluded: chain B residue 40 GLN Chi-restraints excluded: chain B residue 61 LEU Chi-restraints excluded: chain B residue 72 LEU Chi-restraints excluded: chain B residue 113 THR Chi-restraints excluded: chain B residue 131 MET Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 191 LYS Chi-restraints excluded: chain B residue 199 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 4 optimal weight: 2.9990 chunk 42 optimal weight: 0.4980 chunk 11 optimal weight: 2.9990 chunk 3 optimal weight: 4.9990 chunk 17 optimal weight: 4.9990 chunk 37 optimal weight: 4.9990 chunk 30 optimal weight: 0.0030 chunk 16 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 15 optimal weight: 0.7980 chunk 45 optimal weight: 1.9990 overall best weight: 1.0594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.172401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.144056 restraints weight = 5285.732| |-----------------------------------------------------------------------------| r_work (start): 0.3729 rms_B_bonded: 2.38 r_work: 0.3608 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3451 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3451 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7678 moved from start: 0.1960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 4434 Z= 0.246 Angle : 0.616 7.819 6032 Z= 0.304 Chirality : 0.041 0.144 669 Planarity : 0.004 0.036 773 Dihedral : 6.884 55.384 690 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 3.85 % Allowed : 22.01 % Favored : 74.15 % 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: 0.27 (0.38), residues: 521 helix: 2.31 (0.46), residues: 116 sheet: -0.55 (0.36), residues: 210 loop : -0.11 (0.47), residues: 195 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 100 HIS 0.003 0.001 HIS A 85 PHE 0.009 0.001 PHE B 153 TYR 0.010 0.001 TYR B 138 ARG 0.003 0.000 ARG A 60 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1042 Ramachandran restraints generated. 521 Oldfield, 0 Emsley, 521 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1042 Ramachandran restraints generated. 521 Oldfield, 0 Emsley, 521 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 82 time to evaluate : 0.472 Fit side-chains revert: symmetry clash REVERT: A 26 ASN cc_start: 0.8473 (t0) cc_final: 0.8074 (t0) REVERT: A 88 ARG cc_start: 0.8517 (ttp-170) cc_final: 0.8027 (ttp-170) REVERT: B 59 GLU cc_start: 0.6784 (mt-10) cc_final: 0.6313 (pt0) REVERT: B 68 LYS cc_start: 0.8204 (tppt) cc_final: 0.7912 (tppp) REVERT: B 117 GLU cc_start: 0.7217 (pt0) cc_final: 0.6799 (pt0) outliers start: 18 outliers final: 17 residues processed: 92 average time/residue: 0.1729 time to fit residues: 19.9622 Evaluate side-chains 101 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 84 time to evaluate : 0.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 57 TRP Chi-restraints excluded: chain C residue 149 SER Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain B residue 18 SER Chi-restraints excluded: chain B residue 24 LEU Chi-restraints excluded: chain B residue 40 GLN Chi-restraints excluded: chain B residue 61 LEU Chi-restraints excluded: chain B residue 72 LEU Chi-restraints excluded: chain B residue 88 LYS Chi-restraints excluded: chain B residue 113 THR Chi-restraints excluded: chain B residue 131 MET Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 191 LYS Chi-restraints excluded: chain B residue 199 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 13 optimal weight: 0.9980 chunk 9 optimal weight: 2.9990 chunk 33 optimal weight: 3.9990 chunk 19 optimal weight: 0.4980 chunk 31 optimal weight: 0.3980 chunk 47 optimal weight: 0.3980 chunk 43 optimal weight: 0.8980 chunk 6 optimal weight: 0.9990 chunk 50 optimal weight: 0.8980 chunk 42 optimal weight: 0.7980 chunk 45 optimal weight: 0.8980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4072 r_free = 0.4072 target = 0.174243 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.146097 restraints weight = 5363.899| |-----------------------------------------------------------------------------| r_work (start): 0.3760 rms_B_bonded: 2.39 r_work: 0.3640 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3479 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3479 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7644 moved from start: 0.2006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 4434 Z= 0.179 Angle : 0.595 7.936 6032 Z= 0.290 Chirality : 0.040 0.151 669 Planarity : 0.004 0.033 773 Dihedral : 6.751 54.701 690 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 3.21 % Allowed : 22.44 % Favored : 74.36 % 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: 0.35 (0.38), residues: 521 helix: 2.46 (0.47), residues: 116 sheet: -0.52 (0.37), residues: 203 loop : -0.11 (0.46), residues: 202 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP A 100 HIS 0.003 0.001 HIS C 31 PHE 0.007 0.001 PHE B 142 TYR 0.010 0.001 TYR B 138 ARG 0.003 0.000 ARG A 60 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2862.41 seconds wall clock time: 51 minutes 3.08 seconds (3063.08 seconds total)