Starting phenix.real_space_refine on Tue Feb 11 05:44:06 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bpu_44790/02_2025/9bpu_44790.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bpu_44790/02_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_44790/02_2025/9bpu_44790.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bpu_44790/02_2025/9bpu_44790.map" model { file = "/net/cci-nas-00/data/ceres_data/9bpu_44790/02_2025/9bpu_44790.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bpu_44790/02_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-5592/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: 2.97, per 1000 atoms: 0.69 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 535.0 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: 0.61 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: 1.31 Time building geometry restraints manager: 1.36 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: 0.740 Set stop_for_unknowns flag: 0.010 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: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 14.780 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:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.590 ------------------------------------------------------------------------------- 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 : 0.583 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: 0.1674 time to fit residues: 20.4655 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 : 0.482 ------------------------------------------------------------------------------- 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: 0.7980 chunk 24 optimal weight: 1.9990 chunk 29 optimal weight: 3.9990 chunk 46 optimal weight: 3.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- 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 = 0.4073 r_free = 0.4073 target = 0.174324 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.145536 restraints weight = 5392.106| |-----------------------------------------------------------------------------| r_work (start): 0.3758 rms_B_bonded: 2.43 r_work: 0.3640 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3479 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3479 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7638 moved from start: 0.0943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 4434 Z= 0.252 Angle : 0.613 7.057 6032 Z= 0.301 Chirality : 0.042 0.145 669 Planarity : 0.004 0.033 773 Dihedral : 9.526 65.347 690 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 4.49 % Allowed : 21.58 % Favored : 73.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.11 (0.37), residues: 521 helix: 1.95 (0.48), residues: 117 sheet: -0.45 (0.36), residues: 201 loop : -0.33 (0.44), residues: 203 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 0.017 0.002 PHE A 62 TYR 0.015 0.001 TYR B 138 ARG 0.003 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 108 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 87 time to evaluate : 0.474 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 26 ASN cc_start: 0.8444 (t0) cc_final: 0.8203 (t0) REVERT: B 40 GLN cc_start: 0.7909 (OUTLIER) cc_final: 0.7414 (tt0) outliers start: 21 outliers final: 11 residues processed: 98 average time/residue: 0.1681 time to fit residues: 20.7217 Evaluate side-chains 88 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 76 time to evaluate : 0.499 ------------------------------------------------------------------------------- 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 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: 0.6980 chunk 38 optimal weight: 0.6980 chunk 24 optimal weight: 0.7980 chunk 32 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 chunk 31 optimal weight: 3.9990 chunk 12 optimal weight: 0.9990 chunk 0 optimal weight: 7.9990 chunk 36 optimal weight: 5.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- 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 = 0.4062 r_free = 0.4062 target = 0.173280 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.144779 restraints weight = 5341.069| |-----------------------------------------------------------------------------| r_work (start): 0.3744 rms_B_bonded: 2.40 r_work: 0.3622 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3468 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3468 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7651 moved from start: 0.1297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 4434 Z= 0.240 Angle : 0.593 7.099 6032 Z= 0.290 Chirality : 0.042 0.134 669 Planarity : 0.004 0.031 773 Dihedral : 7.710 56.202 690 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 5.13 % Allowed : 19.23 % 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: 0.22 (0.38), residues: 521 helix: 2.34 (0.48), residues: 111 sheet: -0.48 (0.36), residues: 201 loop : -0.27 (0.44), residues: 209 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 152 HIS 0.005 0.001 HIS A 97 PHE 0.012 0.001 PHE A 62 TYR 0.012 0.001 TYR B 99 ARG 0.003 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 103 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 79 time to evaluate : 0.522 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 118 ASP cc_start: 0.7396 (m-30) cc_final: 0.7173 (m-30) REVERT: A 26 ASN cc_start: 0.8511 (t0) cc_final: 0.8001 (t0) REVERT: A 88 ARG cc_start: 0.8535 (ttp-170) cc_final: 0.7968 (ttp-170) REVERT: B 40 GLN cc_start: 0.7933 (OUTLIER) cc_final: 0.7421 (tt0) outliers start: 24 outliers final: 16 residues processed: 93 average time/residue: 0.1702 time to fit residues: 19.9739 Evaluate side-chains 95 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 78 time to evaluate : 0.478 ------------------------------------------------------------------------------- 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 A residue 89 VAL Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 122 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 113 THR Chi-restraints excluded: chain B residue 130 CYS 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 32 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 chunk 12 optimal weight: 0.3980 chunk 10 optimal weight: 3.9990 chunk 17 optimal weight: 4.9990 chunk 14 optimal weight: 0.3980 chunk 20 optimal weight: 4.9990 chunk 27 optimal weight: 4.9990 chunk 25 optimal weight: 0.0170 chunk 11 optimal weight: 0.6980 chunk 8 optimal weight: 0.9990 overall best weight: 0.5020 ------------------------------------------------------------------------------- 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 = 0.4098 r_free = 0.4098 target = 0.176352 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.148393 restraints weight = 5372.257| |-----------------------------------------------------------------------------| r_work (start): 0.3790 rms_B_bonded: 2.39 r_work: 0.3673 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3512 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3512 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7606 moved from start: 0.1400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 4434 Z= 0.154 Angle : 0.550 7.486 6032 Z= 0.267 Chirality : 0.040 0.147 669 Planarity : 0.003 0.031 773 Dihedral : 6.920 54.916 690 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 4.27 % Allowed : 19.87 % Favored : 75.85 % 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: 0.37 (0.38), residues: 521 helix: 2.66 (0.48), residues: 111 sheet: -0.46 (0.37), residues: 194 loop : -0.23 (0.43), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 100 HIS 0.004 0.001 HIS A 97 PHE 0.007 0.001 PHE B 101 TYR 0.011 0.001 TYR B 138 ARG 0.003 0.000 ARG A 60 *********************** 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 97 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 77 time to evaluate : 0.532 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 26 ASN cc_start: 0.8498 (t0) cc_final: 0.8033 (t0) REVERT: A 88 ARG cc_start: 0.8468 (ttp-170) cc_final: 0.7988 (ttp-170) REVERT: B 59 GLU cc_start: 0.6546 (mt-10) cc_final: 0.6092 (pt0) outliers start: 20 outliers final: 12 residues processed: 90 average time/residue: 0.1465 time to fit residues: 16.9258 Evaluate side-chains 81 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 69 time to evaluate : 0.529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 57 TRP Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 122 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 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 40 optimal weight: 5.9990 chunk 41 optimal weight: 0.8980 chunk 16 optimal weight: 5.9990 chunk 24 optimal weight: 0.8980 chunk 19 optimal weight: 0.8980 chunk 14 optimal weight: 0.8980 chunk 12 optimal weight: 2.9990 chunk 33 optimal weight: 0.9990 chunk 35 optimal weight: 0.8980 chunk 30 optimal weight: 0.5980 chunk 8 optimal weight: 3.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 167 GLN ** 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 = 0.4064 r_free = 0.4064 target = 0.174490 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.150986 restraints weight = 5481.842| |-----------------------------------------------------------------------------| r_work (start): 0.3801 rms_B_bonded: 2.05 r_work: 0.3659 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3507 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3507 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7705 moved from start: 0.1561 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= 0.208 Angle : 0.572 6.747 6032 Z= 0.278 Chirality : 0.041 0.142 669 Planarity : 0.004 0.032 773 Dihedral : 6.882 55.224 690 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 5.77 % Allowed : 17.74 % 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: 0.30 (0.38), residues: 521 helix: 2.52 (0.48), residues: 111 sheet: -0.49 (0.36), residues: 201 loop : -0.23 (0.44), residues: 209 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 152 HIS 0.006 0.001 HIS A 97 PHE 0.008 0.001 PHE B 153 TYR 0.010 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 104 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 77 time to evaluate : 0.499 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 ASN cc_start: 0.8388 (t0) cc_final: 0.7995 (t0) REVERT: B 59 GLU cc_start: 0.6535 (mt-10) cc_final: 0.6194 (pt0) outliers start: 27 outliers final: 18 residues processed: 94 average time/residue: 0.1633 time to fit residues: 19.5605 Evaluate side-chains 97 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 79 time to evaluate : 0.457 ------------------------------------------------------------------------------- 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 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 122 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 113 THR 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 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: 0.0980 chunk 43 optimal weight: 6.9990 chunk 40 optimal weight: 3.9990 chunk 42 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 46 optimal weight: 0.9980 chunk 12 optimal weight: 0.9980 chunk 9 optimal weight: 2.9990 chunk 4 optimal weight: 10.0000 chunk 2 optimal weight: 2.9990 chunk 41 optimal weight: 0.9980 overall best weight: 1.2182 ------------------------------------------------------------------------------- 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 = 0.4029 r_free = 0.4029 target = 0.171019 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.144404 restraints weight = 5404.092| |-----------------------------------------------------------------------------| r_work (start): 0.3725 rms_B_bonded: 2.18 r_work: 0.3600 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3444 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3444 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7704 moved from start: 0.1661 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= 0.270 Angle : 0.611 7.530 6032 Z= 0.300 Chirality : 0.042 0.138 669 Planarity : 0.004 0.030 773 Dihedral : 6.993 55.613 690 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 5.56 % Allowed : 18.80 % 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: 0.06 (0.38), residues: 521 helix: 1.93 (0.48), residues: 117 sheet: -0.58 (0.36), residues: 201 loop : -0.26 (0.45), residues: 203 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 152 HIS 0.004 0.001 HIS A 97 PHE 0.010 0.001 PHE B 153 TYR 0.011 0.001 TYR B 99 ARG 0.003 0.000 ARG A 60 *********************** 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 107 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 81 time to evaluate : 0.485 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 26 ASN cc_start: 0.8451 (t0) cc_final: 0.8017 (t0) REVERT: B 59 GLU cc_start: 0.6717 (mt-10) cc_final: 0.6265 (pt0) outliers start: 26 outliers final: 20 residues processed: 99 average time/residue: 0.1753 time to fit residues: 21.7066 Evaluate side-chains 101 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 81 time to evaluate : 0.494 ------------------------------------------------------------------------------- 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 122 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 185 SER 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: 10.0000 chunk 29 optimal weight: 3.9990 chunk 45 optimal weight: 0.9980 chunk 34 optimal weight: 8.9990 chunk 6 optimal weight: 0.5980 chunk 16 optimal weight: 2.9990 chunk 26 optimal weight: 0.9990 chunk 15 optimal weight: 0.0070 chunk 31 optimal weight: 0.4980 chunk 39 optimal weight: 1.9990 overall best weight: 0.6200 ------------------------------------------------------------------------------- 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 = 0.4063 r_free = 0.4063 target = 0.174535 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.151261 restraints weight = 5357.671| |-----------------------------------------------------------------------------| r_work (start): 0.3803 rms_B_bonded: 2.05 r_work: 0.3671 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3520 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3520 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7695 moved from start: 0.1752 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= 0.175 Angle : 0.564 7.427 6032 Z= 0.273 Chirality : 0.040 0.147 669 Planarity : 0.004 0.032 773 Dihedral : 6.771 54.845 690 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 5.13 % Allowed : 19.44 % 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: 0.26 (0.38), residues: 521 helix: 2.18 (0.47), residues: 122 sheet: -0.49 (0.37), residues: 194 loop : -0.24 (0.44), residues: 205 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 100 HIS 0.005 0.001 HIS A 97 PHE 0.007 0.001 PHE B 142 TYR 0.011 0.001 TYR B 138 ARG 0.003 0.000 ARG A 60 *********************** 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 108 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 84 time to evaluate : 0.489 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 26 ASN cc_start: 0.8366 (t0) cc_final: 0.8020 (t0) REVERT: A 88 ARG cc_start: 0.8551 (ttp-170) cc_final: 0.7985 (ttp-170) REVERT: B 59 GLU cc_start: 0.6574 (mt-10) cc_final: 0.6211 (pt0) REVERT: B 68 LYS cc_start: 0.8204 (tppt) cc_final: 0.7899 (tppp) outliers start: 24 outliers final: 17 residues processed: 100 average time/residue: 0.1650 time to fit residues: 20.9269 Evaluate side-chains 96 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 79 time to evaluate : 0.485 ------------------------------------------------------------------------------- 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 C residue 149 SER Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 122 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 191 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 41 optimal weight: 0.9990 chunk 12 optimal weight: 0.6980 chunk 39 optimal weight: 0.7980 chunk 49 optimal weight: 1.9990 chunk 31 optimal weight: 0.0570 chunk 34 optimal weight: 3.9990 chunk 37 optimal weight: 2.9990 chunk 33 optimal weight: 0.7980 chunk 20 optimal weight: 4.9990 chunk 15 optimal weight: 0.7980 chunk 44 optimal weight: 0.0870 overall best weight: 0.4876 ------------------------------------------------------------------------------- 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 = 0.4072 r_free = 0.4072 target = 0.175408 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.149076 restraints weight = 5374.650| |-----------------------------------------------------------------------------| r_work (start): 0.3781 rms_B_bonded: 2.17 r_work: 0.3659 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3503 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3503 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7645 moved from start: 0.1858 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= 0.163 Angle : 0.563 7.427 6032 Z= 0.273 Chirality : 0.040 0.151 669 Planarity : 0.004 0.032 773 Dihedral : 6.669 54.608 690 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 5.13 % Allowed : 20.09 % Favored : 74.79 % 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: 2.23 (0.47), residues: 122 sheet: -0.43 (0.37), residues: 194 loop : -0.17 (0.45), residues: 205 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 100 HIS 0.003 0.001 HIS C 31 PHE 0.006 0.001 PHE B 142 TYR 0.011 0.001 TYR B 35 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: 24 poor density : 77 time to evaluate : 0.486 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 26 ASN cc_start: 0.8386 (t0) cc_final: 0.8007 (t0) REVERT: A 88 ARG cc_start: 0.8528 (ttp-170) cc_final: 0.7848 (ttp-170) REVERT: B 59 GLU cc_start: 0.6657 (mt-10) cc_final: 0.6145 (pt0) REVERT: B 68 LYS cc_start: 0.8261 (tppt) cc_final: 0.7948 (tppp) outliers start: 24 outliers final: 19 residues processed: 92 average time/residue: 0.1835 time to fit residues: 21.1049 Evaluate side-chains 95 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 76 time to evaluate : 0.473 ------------------------------------------------------------------------------- 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 47 LYS Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 122 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 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 191 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 2 optimal weight: 2.9990 chunk 9 optimal weight: 3.9990 chunk 28 optimal weight: 0.6980 chunk 48 optimal weight: 8.9990 chunk 34 optimal weight: 6.9990 chunk 29 optimal weight: 6.9990 chunk 45 optimal weight: 0.8980 chunk 50 optimal weight: 0.9990 chunk 24 optimal weight: 1.9990 chunk 15 optimal weight: 0.0060 chunk 30 optimal weight: 0.5980 overall best weight: 0.6398 ------------------------------------------------------------------------------- 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 = 0.4069 r_free = 0.4069 target = 0.174787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.148008 restraints weight = 5410.344| |-----------------------------------------------------------------------------| r_work (start): 0.3774 rms_B_bonded: 2.21 r_work: 0.3651 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3490 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3490 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7691 moved from start: 0.1877 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= 0.181 Angle : 0.578 7.314 6032 Z= 0.281 Chirality : 0.040 0.149 669 Planarity : 0.004 0.031 773 Dihedral : 6.672 54.732 690 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 4.70 % Allowed : 20.30 % Favored : 75.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.38), residues: 521 helix: 2.24 (0.47), residues: 122 sheet: -0.43 (0.38), residues: 194 loop : -0.19 (0.44), residues: 205 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 100 HIS 0.003 0.001 HIS C 31 PHE 0.006 0.001 PHE B 142 TYR 0.010 0.001 TYR B 138 ARG 0.002 0.000 ARG A 90 *********************** 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: 22 poor density : 78 time to evaluate : 0.548 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 26 ASN cc_start: 0.8398 (t0) cc_final: 0.8040 (t0) REVERT: A 88 ARG cc_start: 0.8538 (ttp-170) cc_final: 0.7916 (ttp-170) REVERT: A 129 MET cc_start: 0.8535 (OUTLIER) cc_final: 0.8291 (mtp) REVERT: B 59 GLU cc_start: 0.6726 (mt-10) cc_final: 0.6425 (pt0) REVERT: B 68 LYS cc_start: 0.8241 (tppt) cc_final: 0.7934 (tppp) REVERT: B 69 LYS cc_start: 0.8030 (pttt) cc_final: 0.7830 (pttt) outliers start: 22 outliers final: 18 residues processed: 92 average time/residue: 0.1831 time to fit residues: 21.4528 Evaluate side-chains 96 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 77 time to evaluate : 0.494 ------------------------------------------------------------------------------- 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 47 LYS 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 A residue 129 MET 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 134 LEU Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 185 SER Chi-restraints excluded: chain B residue 191 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 4 optimal weight: 0.9980 chunk 42 optimal weight: 0.0970 chunk 11 optimal weight: 0.9980 chunk 3 optimal weight: 8.9990 chunk 17 optimal weight: 4.9990 chunk 37 optimal weight: 1.9990 chunk 30 optimal weight: 0.0060 chunk 16 optimal weight: 2.9990 chunk 47 optimal weight: 1.9990 chunk 15 optimal weight: 4.9990 chunk 45 optimal weight: 0.9980 overall best weight: 0.6194 ------------------------------------------------------------------------------- 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 = 0.4068 r_free = 0.4068 target = 0.174787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.149409 restraints weight = 5310.813| |-----------------------------------------------------------------------------| r_work (start): 0.3786 rms_B_bonded: 2.03 r_work: 0.3668 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3515 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3515 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7667 moved from start: 0.1936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4434 Z= 0.182 Angle : 0.586 7.523 6032 Z= 0.285 Chirality : 0.040 0.150 669 Planarity : 0.004 0.031 773 Dihedral : 6.665 54.667 690 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 4.49 % Allowed : 20.94 % 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: 0.42 (0.38), residues: 521 helix: 2.64 (0.46), residues: 116 sheet: -0.39 (0.38), residues: 194 loop : -0.29 (0.44), residues: 211 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 152 HIS 0.003 0.001 HIS A 97 PHE 0.008 0.001 PHE B 101 TYR 0.010 0.001 TYR B 138 ARG 0.001 0.000 ARG A 198 ********************** 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 99 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 78 time to evaluate : 0.518 Fit side-chains revert: symmetry clash REVERT: A 26 ASN cc_start: 0.8360 (t0) cc_final: 0.8014 (t0) REVERT: B 59 GLU cc_start: 0.6680 (mt-10) cc_final: 0.6343 (pt0) REVERT: B 68 LYS cc_start: 0.8209 (tppt) cc_final: 0.7904 (tppp) outliers start: 21 outliers final: 20 residues processed: 92 average time/residue: 0.1718 time to fit residues: 19.9769 Evaluate side-chains 97 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 77 time to evaluate : 0.534 ------------------------------------------------------------------------------- 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 47 LYS 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 22 THR 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 134 LEU Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 185 SER Chi-restraints excluded: chain B residue 191 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 13 optimal weight: 0.6980 chunk 9 optimal weight: 3.9990 chunk 33 optimal weight: 3.9990 chunk 19 optimal weight: 2.9990 chunk 31 optimal weight: 0.9980 chunk 47 optimal weight: 0.8980 chunk 43 optimal weight: 5.9990 chunk 6 optimal weight: 0.9980 chunk 50 optimal weight: 1.9990 chunk 42 optimal weight: 0.8980 chunk 45 optimal weight: 0.5980 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 = 0.4058 r_free = 0.4058 target = 0.173867 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.150174 restraints weight = 5391.741| |-----------------------------------------------------------------------------| r_work (start): 0.3795 rms_B_bonded: 2.04 r_work: 0.3656 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3502 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3502 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7719 moved from start: 0.1983 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= 0.210 Angle : 0.600 7.583 6032 Z= 0.293 Chirality : 0.041 0.146 669 Planarity : 0.004 0.030 773 Dihedral : 6.736 55.004 690 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 4.70 % Allowed : 20.51 % Favored : 74.79 % 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: 0.34 (0.38), residues: 521 helix: 2.19 (0.47), residues: 122 sheet: -0.39 (0.38), residues: 194 loop : -0.20 (0.45), residues: 205 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 100 HIS 0.003 0.001 HIS C 31 PHE 0.008 0.001 PHE B 153 TYR 0.010 0.001 TYR B 138 ARG 0.004 0.000 ARG A 60 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2707.86 seconds wall clock time: 48 minutes 36.38 seconds (2916.38 seconds total)