Starting phenix.real_space_refine on Fri Dec 27 07:48:34 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8gvk_32099/12_2024/8gvk_32099.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gvk_32099/12_2024/8gvk_32099.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8gvk_32099/12_2024/8gvk_32099.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gvk_32099/12_2024/8gvk_32099.map" model { file = "/net/cci-nas-00/data/ceres_data/8gvk_32099/12_2024/8gvk_32099.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gvk_32099/12_2024/8gvk_32099.cif" } resolution = 2.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 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: 3 Type Number sf(0) Gaussians C 2224 2.51 5 N 620 2.21 5 O 723 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 3567 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 887 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 887 Classifications: {'peptide': 119} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 1, 'TRANS': 117} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "B" Number of atoms: 887 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 887 Classifications: {'peptide': 119} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 1, 'TRANS': 117} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "C" Number of atoms: 887 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 887 Classifications: {'peptide': 119} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 1, 'TRANS': 117} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "D" Number of atoms: 887 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 887 Classifications: {'peptide': 119} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 1, 'TRANS': 117} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "C" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "D" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Time building chain proxies: 2.68, per 1000 atoms: 0.75 Number of scatterers: 3567 At special positions: 0 Unit cell: (68.0021, 57.6201, 62.8111, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 3 Type Number sf(0) O 723 8.00 N 620 7.00 C 2224 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.87 Conformation dependent library (CDL) restraints added in 448.3 milliseconds 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 824 Finding SS restraints... Secondary structure from input PDB file: 4 helices and 4 sheets defined 3.4% alpha, 52.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.47 Creating SS restraints... Processing helix chain 'A' and resid 118 through 121 Processing helix chain 'B' and resid 118 through 121 Processing helix chain 'C' and resid 118 through 121 Processing helix chain 'D' and resid 118 through 121 Processing sheet with id=AA1, first strand: chain 'A' and resid 19 through 23 removed outlier: 5.335A pdb=" N VAL A 55 " --> pdb=" O ALA A 78 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N ALA A 78 " --> pdb=" O VAL A 55 " (cutoff:3.500A) removed outlier: 4.992A pdb=" N SER A 88 " --> pdb=" O TRP A 79 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 19 through 23 removed outlier: 5.334A pdb=" N VAL B 55 " --> pdb=" O ALA B 78 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N ALA B 78 " --> pdb=" O VAL B 55 " (cutoff:3.500A) removed outlier: 4.993A pdb=" N SER B 88 " --> pdb=" O TRP B 79 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 19 through 23 removed outlier: 5.335A pdb=" N VAL C 55 " --> pdb=" O ALA C 78 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N ALA C 78 " --> pdb=" O VAL C 55 " (cutoff:3.500A) removed outlier: 4.992A pdb=" N SER C 88 " --> pdb=" O TRP C 79 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 19 through 23 removed outlier: 5.335A pdb=" N VAL D 55 " --> pdb=" O ALA D 78 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N ALA D 78 " --> pdb=" O VAL D 55 " (cutoff:3.500A) removed outlier: 4.992A pdb=" N SER D 88 " --> pdb=" O TRP D 79 " (cutoff:3.500A) 192 hydrogen bonds defined for protein. 516 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: 0.92 Time building geometry restraints manager: 1.00 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.29: 572 1.29 - 1.37: 640 1.37 - 1.44: 524 1.44 - 1.51: 770 1.51 - 1.58: 1130 Bond restraints: 3636 Sorted by residual: bond pdb=" N ARG B 53 " pdb=" CA ARG B 53 " ideal model delta sigma weight residual 1.455 1.485 -0.030 1.22e-02 6.72e+03 5.95e+00 bond pdb=" N ARG C 53 " pdb=" CA ARG C 53 " ideal model delta sigma weight residual 1.455 1.485 -0.030 1.22e-02 6.72e+03 5.95e+00 bond pdb=" N ARG A 53 " pdb=" CA ARG A 53 " ideal model delta sigma weight residual 1.455 1.485 -0.029 1.22e-02 6.72e+03 5.79e+00 bond pdb=" N ARG D 53 " pdb=" CA ARG D 53 " ideal model delta sigma weight residual 1.455 1.485 -0.029 1.22e-02 6.72e+03 5.75e+00 bond pdb=" CB GLU D 101 " pdb=" CG GLU D 101 " ideal model delta sigma weight residual 1.520 1.584 -0.064 3.00e-02 1.11e+03 4.56e+00 ... (remaining 3631 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.37: 4748 2.37 - 4.74: 168 4.74 - 7.11: 32 7.11 - 9.49: 16 9.49 - 11.86: 12 Bond angle restraints: 4976 Sorted by residual: angle pdb=" CA GLU A 101 " pdb=" CB GLU A 101 " pdb=" CG GLU A 101 " ideal model delta sigma weight residual 114.10 125.96 -11.86 2.00e+00 2.50e-01 3.52e+01 angle pdb=" CA GLU C 101 " pdb=" CB GLU C 101 " pdb=" CG GLU C 101 " ideal model delta sigma weight residual 114.10 125.94 -11.84 2.00e+00 2.50e-01 3.50e+01 angle pdb=" CA GLU B 101 " pdb=" CB GLU B 101 " pdb=" CG GLU B 101 " ideal model delta sigma weight residual 114.10 125.94 -11.84 2.00e+00 2.50e-01 3.50e+01 angle pdb=" CA GLU D 101 " pdb=" CB GLU D 101 " pdb=" CG GLU D 101 " ideal model delta sigma weight residual 114.10 125.90 -11.80 2.00e+00 2.50e-01 3.48e+01 angle pdb=" C ALA A 46 " pdb=" N VAL A 47 " pdb=" CA VAL A 47 " ideal model delta sigma weight residual 121.97 131.28 -9.31 1.80e+00 3.09e-01 2.68e+01 ... (remaining 4971 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.70: 1776 16.70 - 33.41: 148 33.41 - 50.11: 44 50.11 - 66.82: 8 66.82 - 83.52: 8 Dihedral angle restraints: 1984 sinusoidal: 664 harmonic: 1320 Sorted by residual: dihedral pdb=" CA ALA C 46 " pdb=" C ALA C 46 " pdb=" N VAL C 47 " pdb=" CA VAL C 47 " ideal model delta harmonic sigma weight residual 180.00 -103.09 -76.91 0 5.00e+00 4.00e-02 2.37e+02 dihedral pdb=" CA ALA B 46 " pdb=" C ALA B 46 " pdb=" N VAL B 47 " pdb=" CA VAL B 47 " ideal model delta harmonic sigma weight residual 180.00 -103.12 -76.88 0 5.00e+00 4.00e-02 2.36e+02 dihedral pdb=" CA ALA A 46 " pdb=" C ALA A 46 " pdb=" N VAL A 47 " pdb=" CA VAL A 47 " ideal model delta harmonic sigma weight residual -180.00 -103.15 -76.85 0 5.00e+00 4.00e-02 2.36e+02 ... (remaining 1981 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 340 0.046 - 0.093: 159 0.093 - 0.139: 41 0.139 - 0.185: 8 0.185 - 0.231: 8 Chirality restraints: 556 Sorted by residual: chirality pdb=" CB ILE B 17 " pdb=" CA ILE B 17 " pdb=" CG1 ILE B 17 " pdb=" CG2 ILE B 17 " both_signs ideal model delta sigma weight residual False 2.64 2.41 0.23 2.00e-01 2.50e+01 1.34e+00 chirality pdb=" CB ILE D 17 " pdb=" CA ILE D 17 " pdb=" CG1 ILE D 17 " pdb=" CG2 ILE D 17 " both_signs ideal model delta sigma weight residual False 2.64 2.41 0.23 2.00e-01 2.50e+01 1.33e+00 chirality pdb=" CB ILE A 17 " pdb=" CA ILE A 17 " pdb=" CG1 ILE A 17 " pdb=" CG2 ILE A 17 " both_signs ideal model delta sigma weight residual False 2.64 2.42 0.23 2.00e-01 2.50e+01 1.31e+00 ... (remaining 553 not shown) Planarity restraints: 624 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU B 101 " -0.013 2.00e-02 2.50e+03 2.58e-02 6.64e+00 pdb=" C GLU B 101 " 0.045 2.00e-02 2.50e+03 pdb=" O GLU B 101 " -0.017 2.00e-02 2.50e+03 pdb=" N ALA B 102 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU D 101 " 0.013 2.00e-02 2.50e+03 2.57e-02 6.60e+00 pdb=" C GLU D 101 " -0.044 2.00e-02 2.50e+03 pdb=" O GLU D 101 " 0.017 2.00e-02 2.50e+03 pdb=" N ALA D 102 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU A 101 " 0.013 2.00e-02 2.50e+03 2.56e-02 6.54e+00 pdb=" C GLU A 101 " -0.044 2.00e-02 2.50e+03 pdb=" O GLU A 101 " 0.017 2.00e-02 2.50e+03 pdb=" N ALA A 102 " 0.015 2.00e-02 2.50e+03 ... (remaining 621 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 76 2.63 - 3.19: 2732 3.19 - 3.76: 6021 3.76 - 4.33: 8262 4.33 - 4.90: 13553 Nonbonded interactions: 30644 Sorted by model distance: nonbonded pdb=" O SER D 69 " pdb=" O HOH D 201 " model vdw 2.057 3.040 nonbonded pdb=" O SER B 69 " pdb=" O HOH B 201 " model vdw 2.178 3.040 nonbonded pdb=" O SER A 69 " pdb=" O HOH A 201 " model vdw 2.219 3.040 nonbonded pdb=" OE2 GLU B 44 " pdb=" NH1 ARG B 53 " model vdw 2.228 3.120 nonbonded pdb=" O SER C 69 " pdb=" O HOH C 201 " model vdw 2.251 3.040 ... (remaining 30639 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 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } 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: 0.390 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: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 12.970 Find NCS groups from input model: 0.090 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:11.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 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 0.064 3636 Z= 0.424 Angle : 1.289 11.858 4976 Z= 0.716 Chirality : 0.059 0.231 556 Planarity : 0.005 0.026 624 Dihedral : 15.347 83.520 1160 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 2.56 % Allowed : 3.42 % Favored : 94.02 % Rotamer: Outliers : 4.07 % Allowed : 5.23 % Favored : 90.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 2.56 % 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: -1.54 (0.33), residues: 468 helix: None (None), residues: 0 sheet: -0.66 (0.27), residues: 264 loop : -1.39 (0.36), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.003 TRP B 108 HIS 0.001 0.000 HIS C 87 PHE 0.011 0.002 PHE C 29 TYR 0.010 0.002 TYR A 96 ARG 0.002 0.000 ARG C 84 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 63 time to evaluate : 0.417 Fit side-chains REVERT: A 52 SER cc_start: 0.6298 (m) cc_final: 0.5932 (m) REVERT: A 103 ARG cc_start: 0.7113 (tpp-160) cc_final: 0.6694 (ttp80) REVERT: A 116 GLU cc_start: 0.6511 (tp30) cc_final: 0.6193 (tm-30) REVERT: A 121 LYS cc_start: 0.7918 (pttt) cc_final: 0.7712 (pttm) REVERT: B 103 ARG cc_start: 0.7139 (tpp-160) cc_final: 0.6742 (ttp80) REVERT: B 116 GLU cc_start: 0.6584 (tp30) cc_final: 0.6301 (tm-30) REVERT: B 121 LYS cc_start: 0.7890 (pttt) cc_final: 0.7644 (pttm) REVERT: C 53 ARG cc_start: 0.6940 (mtt90) cc_final: 0.6548 (mtt-85) REVERT: C 103 ARG cc_start: 0.7130 (tpp-160) cc_final: 0.6711 (ttp80) REVERT: C 116 GLU cc_start: 0.6554 (tp30) cc_final: 0.6307 (tm-30) REVERT: C 121 LYS cc_start: 0.7915 (pttt) cc_final: 0.7677 (pttm) REVERT: D 52 SER cc_start: 0.5883 (m) cc_final: 0.5565 (m) REVERT: D 103 ARG cc_start: 0.7161 (tpp-160) cc_final: 0.6749 (ttp80) REVERT: D 121 LYS cc_start: 0.7906 (pttt) cc_final: 0.7668 (pttm) outliers start: 14 outliers final: 0 residues processed: 71 average time/residue: 1.4300 time to fit residues: 104.2956 Evaluate side-chains 43 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 43 time to evaluate : 0.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 37 optimal weight: 4.9990 chunk 33 optimal weight: 20.0000 chunk 18 optimal weight: 8.9990 chunk 11 optimal weight: 20.0000 chunk 22 optimal weight: 20.0000 chunk 17 optimal weight: 6.9990 chunk 34 optimal weight: 5.9990 chunk 13 optimal weight: 5.9990 chunk 20 optimal weight: 9.9990 chunk 25 optimal weight: 9.9990 chunk 39 optimal weight: 2.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 118 ASN B 107 GLN B 118 ASN B 127 HIS C 107 GLN C 118 ASN C 127 HIS D 118 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.2196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.040 3636 Z= 0.378 Angle : 0.945 7.855 4976 Z= 0.508 Chirality : 0.051 0.163 556 Planarity : 0.005 0.046 624 Dihedral : 9.641 67.032 512 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 10.19 Ramachandran Plot: Outliers : 2.56 % Allowed : 4.27 % Favored : 93.16 % Rotamer: Outliers : 5.52 % Allowed : 10.47 % Favored : 84.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 1.71 % 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: -1.29 (0.33), residues: 468 helix: -4.62 (0.30), residues: 24 sheet: 0.07 (0.25), residues: 284 loop : -1.84 (0.42), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.003 TRP D 79 HIS 0.002 0.001 HIS B 87 PHE 0.014 0.003 PHE A 29 TYR 0.010 0.002 TYR D 83 ARG 0.004 0.001 ARG C 84 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 49 time to evaluate : 0.474 Fit side-chains REVERT: A 52 SER cc_start: 0.6155 (m) cc_final: 0.5742 (m) REVERT: A 53 ARG cc_start: 0.7121 (ttm110) cc_final: 0.6625 (mtt-85) REVERT: A 103 ARG cc_start: 0.7128 (tpp-160) cc_final: 0.6648 (ttp80) REVERT: A 121 LYS cc_start: 0.7892 (pttt) cc_final: 0.7654 (pttp) REVERT: B 52 SER cc_start: 0.6150 (OUTLIER) cc_final: 0.5513 (m) REVERT: B 53 ARG cc_start: 0.7078 (ttm110) cc_final: 0.6542 (mtt-85) REVERT: B 103 ARG cc_start: 0.7136 (tpp-160) cc_final: 0.6666 (ttp80) REVERT: B 121 LYS cc_start: 0.7887 (pttt) cc_final: 0.7641 (pttp) REVERT: C 52 SER cc_start: 0.6208 (OUTLIER) cc_final: 0.5572 (m) REVERT: C 53 ARG cc_start: 0.7069 (mtt90) cc_final: 0.6596 (mtt-85) REVERT: C 103 ARG cc_start: 0.7131 (tpp-160) cc_final: 0.6654 (ttp80) REVERT: C 121 LYS cc_start: 0.7899 (pttt) cc_final: 0.7656 (pttp) REVERT: D 52 SER cc_start: 0.6127 (m) cc_final: 0.5719 (m) REVERT: D 53 ARG cc_start: 0.7118 (ttm110) cc_final: 0.6541 (mtt-85) REVERT: D 103 ARG cc_start: 0.7128 (tpp-160) cc_final: 0.6670 (ttp80) REVERT: D 121 LYS cc_start: 0.7874 (pttt) cc_final: 0.7631 (pttp) outliers start: 19 outliers final: 7 residues processed: 66 average time/residue: 1.5295 time to fit residues: 103.6530 Evaluate side-chains 50 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 41 time to evaluate : 0.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 SER Chi-restraints excluded: chain B residue 52 SER Chi-restraints excluded: chain B residue 69 SER Chi-restraints excluded: chain C residue 52 SER Chi-restraints excluded: chain C residue 62 SER Chi-restraints excluded: chain C residue 69 SER Chi-restraints excluded: chain D residue 28 THR Chi-restraints excluded: chain D residue 62 SER Chi-restraints excluded: chain D residue 69 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 22 optimal weight: 20.0000 chunk 12 optimal weight: 8.9990 chunk 33 optimal weight: 20.0000 chunk 27 optimal weight: 10.0000 chunk 11 optimal weight: 5.9990 chunk 40 optimal weight: 20.0000 chunk 43 optimal weight: 4.9990 chunk 35 optimal weight: 6.9990 chunk 39 optimal weight: 1.9990 chunk 13 optimal weight: 5.9990 chunk 32 optimal weight: 5.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 107 GLN D 107 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.2690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 3636 Z= 0.355 Angle : 0.917 7.629 4976 Z= 0.490 Chirality : 0.050 0.184 556 Planarity : 0.005 0.045 624 Dihedral : 9.148 62.815 512 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.85 % Allowed : 4.70 % Favored : 94.44 % Rotamer: Outliers : 4.94 % Allowed : 15.70 % Favored : 79.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.85 % 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: -1.07 (0.34), residues: 468 helix: -4.51 (0.36), residues: 24 sheet: 0.32 (0.26), residues: 288 loop : -2.00 (0.42), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.003 TRP D 79 HIS 0.002 0.001 HIS B 87 PHE 0.012 0.003 PHE A 29 TYR 0.008 0.002 TYR A 96 ARG 0.002 0.000 ARG C 84 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 47 time to evaluate : 0.367 Fit side-chains REVERT: A 52 SER cc_start: 0.6244 (m) cc_final: 0.5777 (m) REVERT: A 103 ARG cc_start: 0.7091 (tpp-160) cc_final: 0.6674 (ttp80) REVERT: A 121 LYS cc_start: 0.7856 (pttt) cc_final: 0.7619 (pttp) REVERT: B 52 SER cc_start: 0.6185 (OUTLIER) cc_final: 0.5551 (m) REVERT: B 103 ARG cc_start: 0.7080 (tpp-160) cc_final: 0.6680 (ttp80) REVERT: B 121 LYS cc_start: 0.7848 (pttt) cc_final: 0.7606 (pttp) REVERT: C 52 SER cc_start: 0.6168 (OUTLIER) cc_final: 0.5556 (m) REVERT: C 53 ARG cc_start: 0.7042 (mtt90) cc_final: 0.6580 (mtt-85) REVERT: C 103 ARG cc_start: 0.7074 (tpp-160) cc_final: 0.6669 (ttp80) REVERT: C 121 LYS cc_start: 0.7851 (pttt) cc_final: 0.7616 (pttp) REVERT: D 52 SER cc_start: 0.6266 (m) cc_final: 0.5807 (m) REVERT: D 103 ARG cc_start: 0.7081 (tpp-160) cc_final: 0.6680 (ttp80) REVERT: D 121 LYS cc_start: 0.7839 (pttt) cc_final: 0.7598 (pttp) outliers start: 17 outliers final: 8 residues processed: 61 average time/residue: 1.3310 time to fit residues: 83.5462 Evaluate side-chains 54 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 44 time to evaluate : 0.893 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 SER Chi-restraints excluded: chain B residue 52 SER Chi-restraints excluded: chain B residue 62 SER Chi-restraints excluded: chain B residue 69 SER Chi-restraints excluded: chain C residue 52 SER Chi-restraints excluded: chain C residue 62 SER Chi-restraints excluded: chain C residue 69 SER Chi-restraints excluded: chain D residue 28 THR Chi-restraints excluded: chain D residue 62 SER Chi-restraints excluded: chain D residue 69 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 39 optimal weight: 2.9990 chunk 30 optimal weight: 0.8980 chunk 20 optimal weight: 9.9990 chunk 4 optimal weight: 2.9990 chunk 19 optimal weight: 5.9990 chunk 26 optimal weight: 9.9990 chunk 40 optimal weight: 6.9990 chunk 42 optimal weight: 2.9990 chunk 38 optimal weight: 8.9990 chunk 11 optimal weight: 20.0000 chunk 35 optimal weight: 5.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 moved from start: 0.2785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 3636 Z= 0.251 Angle : 0.816 7.082 4976 Z= 0.431 Chirality : 0.046 0.169 556 Planarity : 0.004 0.039 624 Dihedral : 8.452 58.218 512 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.85 % Allowed : 5.13 % Favored : 94.02 % Rotamer: Outliers : 3.20 % Allowed : 17.73 % Favored : 79.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.85 % 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: -0.87 (0.34), residues: 468 helix: -4.43 (0.40), residues: 24 sheet: 0.44 (0.26), residues: 288 loop : -1.85 (0.42), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.003 TRP D 79 HIS 0.001 0.001 HIS B 87 PHE 0.011 0.003 PHE A 29 TYR 0.010 0.002 TYR A 96 ARG 0.001 0.000 ARG C 84 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 44 time to evaluate : 0.468 Fit side-chains REVERT: A 52 SER cc_start: 0.6237 (m) cc_final: 0.5736 (m) REVERT: A 103 ARG cc_start: 0.7032 (tpp-160) cc_final: 0.6663 (ttp80) REVERT: A 121 LYS cc_start: 0.7844 (pttt) cc_final: 0.7579 (pttp) REVERT: B 52 SER cc_start: 0.6244 (OUTLIER) cc_final: 0.5615 (m) REVERT: B 103 ARG cc_start: 0.7027 (tpp-160) cc_final: 0.6663 (ttp80) REVERT: B 121 LYS cc_start: 0.7843 (pttt) cc_final: 0.7575 (pttp) REVERT: C 52 SER cc_start: 0.6222 (OUTLIER) cc_final: 0.5596 (m) REVERT: C 53 ARG cc_start: 0.7036 (mtt90) cc_final: 0.6569 (mtt-85) REVERT: C 103 ARG cc_start: 0.7027 (tpp-160) cc_final: 0.6653 (ttp80) REVERT: C 121 LYS cc_start: 0.7848 (pttt) cc_final: 0.7581 (pttp) REVERT: D 52 SER cc_start: 0.6207 (m) cc_final: 0.5705 (m) REVERT: D 103 ARG cc_start: 0.7030 (tpp-160) cc_final: 0.6662 (ttp80) REVERT: D 121 LYS cc_start: 0.7835 (pttt) cc_final: 0.7567 (pttp) outliers start: 11 outliers final: 5 residues processed: 49 average time/residue: 1.5614 time to fit residues: 78.7064 Evaluate side-chains 51 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 44 time to evaluate : 0.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 SER Chi-restraints excluded: chain B residue 52 SER Chi-restraints excluded: chain B residue 69 SER Chi-restraints excluded: chain C residue 52 SER Chi-restraints excluded: chain C residue 69 SER Chi-restraints excluded: chain D residue 28 THR Chi-restraints excluded: chain D residue 69 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 24 optimal weight: 10.0000 chunk 0 optimal weight: 20.0000 chunk 31 optimal weight: 9.9990 chunk 17 optimal weight: 10.0000 chunk 36 optimal weight: 0.0170 chunk 29 optimal weight: 20.0000 chunk 21 optimal weight: 5.9990 chunk 38 optimal weight: 9.9990 chunk 10 optimal weight: 3.9990 chunk 14 optimal weight: 10.0000 chunk 8 optimal weight: 1.9990 overall best weight: 4.4026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7950 moved from start: 0.2988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 3636 Z= 0.323 Angle : 0.867 7.492 4976 Z= 0.460 Chirality : 0.048 0.159 556 Planarity : 0.005 0.040 624 Dihedral : 8.300 52.279 512 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.85 % Allowed : 5.13 % Favored : 94.02 % Rotamer: Outliers : 6.40 % Allowed : 14.83 % Favored : 78.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.85 % 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: -0.94 (0.33), residues: 468 helix: -4.31 (0.45), residues: 24 sheet: 0.40 (0.26), residues: 288 loop : -1.94 (0.41), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.003 TRP D 79 HIS 0.001 0.001 HIS C 87 PHE 0.012 0.003 PHE C 29 TYR 0.010 0.002 TYR B 96 ARG 0.002 0.000 ARG C 103 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 44 time to evaluate : 0.350 Fit side-chains REVERT: A 52 SER cc_start: 0.6231 (m) cc_final: 0.5702 (m) REVERT: A 103 ARG cc_start: 0.7061 (tpp-160) cc_final: 0.6667 (ttp80) REVERT: A 121 LYS cc_start: 0.7847 (pttt) cc_final: 0.7619 (pttp) REVERT: B 52 SER cc_start: 0.6269 (OUTLIER) cc_final: 0.5621 (m) REVERT: B 103 ARG cc_start: 0.7064 (tpp-160) cc_final: 0.6667 (ttp80) REVERT: B 121 LYS cc_start: 0.7837 (pttt) cc_final: 0.7605 (pttp) REVERT: C 52 SER cc_start: 0.6217 (OUTLIER) cc_final: 0.5572 (m) REVERT: C 53 ARG cc_start: 0.7074 (mtt90) cc_final: 0.6598 (mtt-85) REVERT: C 103 ARG cc_start: 0.7066 (tpp-160) cc_final: 0.6659 (ttp80) REVERT: C 121 LYS cc_start: 0.7842 (pttt) cc_final: 0.7611 (pttp) REVERT: D 52 SER cc_start: 0.6239 (m) cc_final: 0.5710 (m) REVERT: D 103 ARG cc_start: 0.7077 (tpp-160) cc_final: 0.6673 (ttp80) REVERT: D 121 LYS cc_start: 0.7818 (pttt) cc_final: 0.7590 (pttp) outliers start: 22 outliers final: 10 residues processed: 60 average time/residue: 1.3005 time to fit residues: 80.5464 Evaluate side-chains 56 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 44 time to evaluate : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 69 SER Chi-restraints excluded: chain B residue 52 SER Chi-restraints excluded: chain B residue 69 SER Chi-restraints excluded: chain C residue 39 LEU Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 52 SER Chi-restraints excluded: chain C residue 69 SER Chi-restraints excluded: chain D residue 28 THR Chi-restraints excluded: chain D residue 39 LEU Chi-restraints excluded: chain D residue 47 VAL Chi-restraints excluded: chain D residue 69 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 24 optimal weight: 6.9990 chunk 10 optimal weight: 4.9990 chunk 42 optimal weight: 10.0000 chunk 35 optimal weight: 10.0000 chunk 19 optimal weight: 5.9990 chunk 3 optimal weight: 9.9990 chunk 14 optimal weight: 9.9990 chunk 22 optimal weight: 20.0000 chunk 41 optimal weight: 1.9990 chunk 4 optimal weight: 0.4980 chunk 31 optimal weight: 9.9990 overall best weight: 4.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7947 moved from start: 0.3038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 3636 Z= 0.302 Angle : 0.853 7.558 4976 Z= 0.451 Chirality : 0.048 0.148 556 Planarity : 0.004 0.038 624 Dihedral : 7.721 42.432 512 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 1.71 % Allowed : 5.13 % Favored : 93.16 % Rotamer: Outliers : 4.36 % Allowed : 16.57 % Favored : 79.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.85 % 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: -0.92 (0.33), residues: 468 helix: -4.36 (0.43), residues: 24 sheet: 0.39 (0.25), residues: 288 loop : -1.87 (0.42), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.003 TRP D 79 HIS 0.001 0.001 HIS C 87 PHE 0.012 0.003 PHE D 29 TYR 0.011 0.002 TYR B 96 ARG 0.002 0.000 ARG A 103 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 44 time to evaluate : 0.401 Fit side-chains REVERT: A 52 SER cc_start: 0.6250 (m) cc_final: 0.5695 (m) REVERT: A 103 ARG cc_start: 0.7051 (tpp-160) cc_final: 0.6705 (ttp80) REVERT: A 121 LYS cc_start: 0.7831 (pttt) cc_final: 0.7573 (pttp) REVERT: B 52 SER cc_start: 0.6306 (OUTLIER) cc_final: 0.5636 (m) REVERT: B 103 ARG cc_start: 0.7050 (tpp-160) cc_final: 0.6702 (ttp80) REVERT: B 121 LYS cc_start: 0.7820 (pttt) cc_final: 0.7557 (pttp) REVERT: C 52 SER cc_start: 0.6243 (OUTLIER) cc_final: 0.5581 (m) REVERT: C 53 ARG cc_start: 0.7070 (mtt90) cc_final: 0.6604 (mtt-85) REVERT: C 103 ARG cc_start: 0.7048 (tpp-160) cc_final: 0.6691 (ttp80) REVERT: C 121 LYS cc_start: 0.7837 (pttt) cc_final: 0.7577 (pttp) REVERT: D 52 SER cc_start: 0.6243 (m) cc_final: 0.5701 (m) REVERT: D 103 ARG cc_start: 0.7048 (tpp-160) cc_final: 0.6697 (ttp80) REVERT: D 121 LYS cc_start: 0.7826 (pttt) cc_final: 0.7559 (pttp) outliers start: 15 outliers final: 9 residues processed: 53 average time/residue: 1.4010 time to fit residues: 76.5096 Evaluate side-chains 55 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 44 time to evaluate : 0.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 69 SER Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 52 SER Chi-restraints excluded: chain B residue 69 SER Chi-restraints excluded: chain C residue 39 LEU Chi-restraints excluded: chain C residue 52 SER Chi-restraints excluded: chain C residue 69 SER Chi-restraints excluded: chain D residue 28 THR Chi-restraints excluded: chain D residue 39 LEU Chi-restraints excluded: chain D residue 69 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 24 optimal weight: 0.9990 chunk 35 optimal weight: 6.9990 chunk 23 optimal weight: 0.9990 chunk 42 optimal weight: 0.0770 chunk 26 optimal weight: 7.9990 chunk 25 optimal weight: 5.9990 chunk 19 optimal weight: 4.9990 chunk 16 optimal weight: 0.9990 chunk 12 optimal weight: 0.9990 chunk 8 optimal weight: 4.9990 chunk 28 optimal weight: 4.9990 overall best weight: 0.8146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 moved from start: 0.3039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 3636 Z= 0.147 Angle : 0.691 5.848 4976 Z= 0.365 Chirality : 0.043 0.138 556 Planarity : 0.003 0.021 624 Dihedral : 6.229 27.524 512 Min Nonbonded Distance : 2.639 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.85 % Allowed : 5.13 % Favored : 94.02 % Rotamer: Outliers : 2.62 % Allowed : 18.90 % Favored : 78.49 % 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: -0.67 (0.35), residues: 468 helix: -4.85 (0.23), residues: 24 sheet: 0.54 (0.27), residues: 288 loop : -1.52 (0.44), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 108 HIS 0.000 0.000 HIS A 127 PHE 0.008 0.002 PHE C 29 TYR 0.012 0.001 TYR A 96 ARG 0.003 0.000 ARG A 84 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 65 time to evaluate : 0.396 Fit side-chains REVERT: A 52 SER cc_start: 0.6396 (m) cc_final: 0.5842 (m) REVERT: A 88 SER cc_start: 0.8778 (p) cc_final: 0.8482 (m) REVERT: A 103 ARG cc_start: 0.6976 (tpp-160) cc_final: 0.6704 (ttp80) REVERT: A 121 LYS cc_start: 0.7835 (pttt) cc_final: 0.7630 (pttm) REVERT: B 52 SER cc_start: 0.6350 (OUTLIER) cc_final: 0.5775 (m) REVERT: B 84 ARG cc_start: 0.7138 (mtt90) cc_final: 0.6783 (mtm180) REVERT: B 88 SER cc_start: 0.8783 (p) cc_final: 0.8495 (m) REVERT: B 103 ARG cc_start: 0.6968 (tpp-160) cc_final: 0.6709 (ttp80) REVERT: B 121 LYS cc_start: 0.7831 (pttt) cc_final: 0.7623 (pttm) REVERT: C 39 LEU cc_start: 0.7918 (OUTLIER) cc_final: 0.7664 (mp) REVERT: C 52 SER cc_start: 0.6337 (OUTLIER) cc_final: 0.5696 (m) REVERT: C 53 ARG cc_start: 0.7039 (mtt90) cc_final: 0.6595 (mtt-85) REVERT: C 88 SER cc_start: 0.8795 (p) cc_final: 0.8503 (m) REVERT: C 103 ARG cc_start: 0.6970 (tpp-160) cc_final: 0.6701 (ttp80) REVERT: C 121 LYS cc_start: 0.7835 (pttt) cc_final: 0.7634 (pttm) REVERT: D 52 SER cc_start: 0.6355 (m) cc_final: 0.5871 (m) REVERT: D 84 ARG cc_start: 0.7127 (mtt90) cc_final: 0.6775 (mtm180) REVERT: D 88 SER cc_start: 0.8804 (p) cc_final: 0.8502 (m) REVERT: D 103 ARG cc_start: 0.6975 (tpp-160) cc_final: 0.6700 (ttp80) REVERT: D 121 LYS cc_start: 0.7826 (pttt) cc_final: 0.7615 (pttm) outliers start: 9 outliers final: 2 residues processed: 68 average time/residue: 1.0951 time to fit residues: 77.0650 Evaluate side-chains 58 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 53 time to evaluate : 0.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 52 SER Chi-restraints excluded: chain C residue 39 LEU Chi-restraints excluded: chain C residue 52 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 20 optimal weight: 10.0000 chunk 3 optimal weight: 0.0870 chunk 33 optimal weight: 20.0000 chunk 38 optimal weight: 9.9990 chunk 40 optimal weight: 6.9990 chunk 37 optimal weight: 10.0000 chunk 39 optimal weight: 5.9990 chunk 23 optimal weight: 5.9990 chunk 17 optimal weight: 10.0000 chunk 31 optimal weight: 0.0970 chunk 12 optimal weight: 7.9990 overall best weight: 3.8362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 moved from start: 0.3109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 3636 Z= 0.295 Angle : 0.801 7.267 4976 Z= 0.429 Chirality : 0.048 0.145 556 Planarity : 0.004 0.036 624 Dihedral : 6.805 25.179 512 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.85 % Allowed : 5.98 % Favored : 93.16 % Rotamer: Outliers : 3.78 % Allowed : 19.48 % Favored : 76.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.86 (0.34), residues: 468 helix: -4.61 (0.32), residues: 24 sheet: 0.43 (0.26), residues: 288 loop : -1.76 (0.42), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.003 TRP D 120 HIS 0.001 0.001 HIS C 87 PHE 0.008 0.002 PHE D 29 TYR 0.013 0.002 TYR C 96 ARG 0.002 0.000 ARG C 84 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 48 time to evaluate : 0.393 Fit side-chains REVERT: A 52 SER cc_start: 0.6222 (m) cc_final: 0.5648 (m) REVERT: A 103 ARG cc_start: 0.7044 (tpp-160) cc_final: 0.6707 (ttp80) REVERT: A 121 LYS cc_start: 0.7836 (pttt) cc_final: 0.7579 (pttp) REVERT: B 52 SER cc_start: 0.6266 (OUTLIER) cc_final: 0.5596 (m) REVERT: B 103 ARG cc_start: 0.7050 (tpp-160) cc_final: 0.6707 (ttp80) REVERT: B 121 LYS cc_start: 0.7832 (pttt) cc_final: 0.7570 (pttp) REVERT: C 52 SER cc_start: 0.6209 (OUTLIER) cc_final: 0.5559 (m) REVERT: C 53 ARG cc_start: 0.7056 (mtt90) cc_final: 0.6508 (mtm-85) REVERT: C 103 ARG cc_start: 0.7051 (tpp-160) cc_final: 0.6696 (ttp80) REVERT: C 121 LYS cc_start: 0.7836 (pttt) cc_final: 0.7576 (pttp) REVERT: D 52 SER cc_start: 0.6249 (m) cc_final: 0.5671 (m) REVERT: D 103 ARG cc_start: 0.7048 (tpp-160) cc_final: 0.6703 (ttp80) REVERT: D 121 LYS cc_start: 0.7814 (pttt) cc_final: 0.7548 (pttp) outliers start: 13 outliers final: 6 residues processed: 54 average time/residue: 1.3741 time to fit residues: 76.2856 Evaluate side-chains 56 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 48 time to evaluate : 0.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 69 SER Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 52 SER Chi-restraints excluded: chain B residue 69 SER Chi-restraints excluded: chain C residue 39 LEU Chi-restraints excluded: chain C residue 52 SER Chi-restraints excluded: chain D residue 28 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 35 optimal weight: 10.0000 chunk 37 optimal weight: 9.9990 chunk 39 optimal weight: 2.9990 chunk 25 optimal weight: 8.9990 chunk 41 optimal weight: 1.9990 chunk 19 optimal weight: 3.9990 chunk 29 optimal weight: 3.9990 chunk 43 optimal weight: 7.9990 chunk 40 optimal weight: 2.9990 chunk 34 optimal weight: 9.9990 chunk 3 optimal weight: 0.2980 overall best weight: 2.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.3107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3636 Z= 0.223 Angle : 0.755 6.823 4976 Z= 0.404 Chirality : 0.045 0.136 556 Planarity : 0.004 0.031 624 Dihedral : 6.552 24.236 512 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.85 % Allowed : 5.98 % Favored : 93.16 % Rotamer: Outliers : 2.91 % Allowed : 20.06 % Favored : 77.03 % 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: -0.85 (0.34), residues: 468 helix: -4.74 (0.27), residues: 24 sheet: 0.44 (0.26), residues: 288 loop : -1.74 (0.42), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP D 108 HIS 0.001 0.000 HIS C 87 PHE 0.008 0.002 PHE D 29 TYR 0.013 0.002 TYR C 96 ARG 0.004 0.001 ARG D 84 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 45 time to evaluate : 0.318 Fit side-chains REVERT: A 52 SER cc_start: 0.6281 (m) cc_final: 0.5729 (m) REVERT: A 103 ARG cc_start: 0.7026 (tpp-160) cc_final: 0.6717 (ttp80) REVERT: A 121 LYS cc_start: 0.7827 (pttt) cc_final: 0.7595 (pttp) REVERT: B 52 SER cc_start: 0.6219 (OUTLIER) cc_final: 0.5555 (m) REVERT: B 103 ARG cc_start: 0.7028 (tpp-160) cc_final: 0.6718 (ttp80) REVERT: B 121 LYS cc_start: 0.7823 (pttt) cc_final: 0.7588 (pttp) REVERT: C 39 LEU cc_start: 0.7973 (OUTLIER) cc_final: 0.7619 (mp) REVERT: C 52 SER cc_start: 0.6253 (OUTLIER) cc_final: 0.5612 (m) REVERT: C 53 ARG cc_start: 0.7049 (mtt90) cc_final: 0.6527 (mtm-85) REVERT: C 103 ARG cc_start: 0.7028 (tpp-160) cc_final: 0.6711 (ttp80) REVERT: C 121 LYS cc_start: 0.7829 (pttt) cc_final: 0.7596 (pttp) REVERT: D 52 SER cc_start: 0.6240 (m) cc_final: 0.5647 (m) REVERT: D 103 ARG cc_start: 0.7027 (tpp-160) cc_final: 0.6714 (ttp80) REVERT: D 121 LYS cc_start: 0.7818 (pttt) cc_final: 0.7579 (pttp) outliers start: 10 outliers final: 7 residues processed: 50 average time/residue: 1.4709 time to fit residues: 75.4946 Evaluate side-chains 55 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 45 time to evaluate : 0.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 69 SER Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 52 SER Chi-restraints excluded: chain B residue 69 SER Chi-restraints excluded: chain C residue 39 LEU Chi-restraints excluded: chain C residue 52 SER Chi-restraints excluded: chain D residue 28 THR Chi-restraints excluded: chain D residue 39 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 26 optimal weight: 10.0000 chunk 21 optimal weight: 1.9990 chunk 27 optimal weight: 0.8980 chunk 37 optimal weight: 9.9990 chunk 10 optimal weight: 0.0050 chunk 32 optimal weight: 0.9990 chunk 5 optimal weight: 9.9990 chunk 9 optimal weight: 3.9990 chunk 34 optimal weight: 10.0000 chunk 14 optimal weight: 0.9990 chunk 35 optimal weight: 0.9980 overall best weight: 0.7798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7879 moved from start: 0.3169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 3636 Z= 0.147 Angle : 0.658 5.767 4976 Z= 0.354 Chirality : 0.043 0.138 556 Planarity : 0.003 0.017 624 Dihedral : 5.958 25.071 512 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.85 % Allowed : 3.42 % Favored : 95.73 % Rotamer: Outliers : 2.91 % Allowed : 20.35 % Favored : 76.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.78 (0.35), residues: 468 helix: -5.08 (0.16), residues: 24 sheet: 0.49 (0.27), residues: 288 loop : -1.62 (0.43), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP D 108 HIS 0.000 0.000 HIS A 127 PHE 0.005 0.001 PHE D 130 TYR 0.012 0.001 TYR B 96 ARG 0.004 0.001 ARG C 84 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 64 time to evaluate : 0.359 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 32 THR cc_start: 0.7919 (m) cc_final: 0.7624 (t) REVERT: A 52 SER cc_start: 0.6263 (m) cc_final: 0.5694 (m) REVERT: A 88 SER cc_start: 0.8737 (p) cc_final: 0.8507 (m) REVERT: A 103 ARG cc_start: 0.6979 (tpp-160) cc_final: 0.6714 (ttp80) REVERT: A 121 LYS cc_start: 0.7839 (pttt) cc_final: 0.7573 (pttp) REVERT: B 32 THR cc_start: 0.7914 (m) cc_final: 0.7611 (t) REVERT: B 52 SER cc_start: 0.6347 (OUTLIER) cc_final: 0.5774 (m) REVERT: B 84 ARG cc_start: 0.7123 (mtt90) cc_final: 0.6757 (mtm180) REVERT: B 88 SER cc_start: 0.8743 (p) cc_final: 0.8512 (m) REVERT: B 103 ARG cc_start: 0.6980 (tpp-160) cc_final: 0.6719 (ttp80) REVERT: B 121 LYS cc_start: 0.7830 (pttt) cc_final: 0.7562 (pttp) REVERT: C 32 THR cc_start: 0.7902 (m) cc_final: 0.7600 (t) REVERT: C 39 LEU cc_start: 0.7896 (OUTLIER) cc_final: 0.7649 (mp) REVERT: C 52 SER cc_start: 0.6335 (OUTLIER) cc_final: 0.5703 (m) REVERT: C 53 ARG cc_start: 0.7057 (mtt90) cc_final: 0.6670 (mtt-85) REVERT: C 88 SER cc_start: 0.8754 (p) cc_final: 0.8518 (m) REVERT: C 103 ARG cc_start: 0.6983 (tpp-160) cc_final: 0.6713 (ttp80) REVERT: C 121 LYS cc_start: 0.7837 (pttt) cc_final: 0.7574 (pttp) REVERT: D 32 THR cc_start: 0.7901 (m) cc_final: 0.7591 (t) REVERT: D 52 SER cc_start: 0.6167 (m) cc_final: 0.5588 (m) REVERT: D 88 SER cc_start: 0.8765 (p) cc_final: 0.8517 (m) REVERT: D 103 ARG cc_start: 0.6984 (tpp-160) cc_final: 0.6719 (ttp80) REVERT: D 121 LYS cc_start: 0.7816 (pttt) cc_final: 0.7543 (pttp) outliers start: 10 outliers final: 3 residues processed: 64 average time/residue: 1.1522 time to fit residues: 76.1863 Evaluate side-chains 70 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 64 time to evaluate : 0.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 52 SER Chi-restraints excluded: chain C residue 39 LEU Chi-restraints excluded: chain C residue 52 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 4 optimal weight: 3.9990 chunk 6 optimal weight: 10.0000 chunk 30 optimal weight: 0.0870 chunk 1 optimal weight: 8.9990 chunk 25 optimal weight: 8.9990 chunk 40 optimal weight: 10.0000 chunk 23 optimal weight: 5.9990 chunk 29 optimal weight: 20.0000 chunk 27 optimal weight: 9.9990 chunk 26 optimal weight: 0.7980 chunk 17 optimal weight: 0.9990 overall best weight: 2.3764 ------------------------------------------------------------------------------- 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 = 0.3975 r_free = 0.3975 target = 0.171675 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.140874 restraints weight = 3017.496| |-----------------------------------------------------------------------------| r_work (start): 0.3613 rms_B_bonded: 1.40 r_work: 0.3472 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.3346 rms_B_bonded: 3.36 restraints_weight: 0.2500 r_work (final): 0.3346 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8369 moved from start: 0.3130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3636 Z= 0.218 Angle : 0.737 6.551 4976 Z= 0.395 Chirality : 0.045 0.136 556 Planarity : 0.003 0.027 624 Dihedral : 6.341 25.415 512 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.85 % Allowed : 5.77 % Favored : 93.38 % Rotamer: Outliers : 3.20 % Allowed : 20.06 % Favored : 76.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.76 (0.35), residues: 468 helix: -4.97 (0.18), residues: 24 sheet: 0.52 (0.27), residues: 288 loop : -1.67 (0.42), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP D 108 HIS 0.001 0.000 HIS D 87 PHE 0.005 0.002 PHE B 130 TYR 0.014 0.002 TYR A 22 ARG 0.001 0.000 ARG D 59 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1849.15 seconds wall clock time: 34 minutes 25.44 seconds (2065.44 seconds total)