Starting phenix.real_space_refine on Tue Feb 11 00:54:25 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8gvk_32099/02_2025/8gvk_32099.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gvk_32099/02_2025/8gvk_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_32099/02_2025/8gvk_32099.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gvk_32099/02_2025/8gvk_32099.map" model { file = "/net/cci-nas-00/data/ceres_data/8gvk_32099/02_2025/8gvk_32099.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gvk_32099/02_2025/8gvk_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-5592/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: 2.86, per 1000 atoms: 0.80 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 464.4 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: 0.48 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: 1.07 Time building geometry restraints manager: 1.02 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' 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: 0.340 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 13.800 Find NCS groups from input model: 0.080 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:12.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.370 ------------------------------------------------------------------------------- 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 : 0.364 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: 1.3446 time to fit residues: 98.0974 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 : 0.384 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.171370 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.139850 restraints weight = 3066.378| |-----------------------------------------------------------------------------| r_work (start): 0.3598 rms_B_bonded: 1.40 r_work: 0.3450 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3326 rms_B_bonded: 3.41 restraints_weight: 0.2500 r_work (final): 0.3326 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8381 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 : 0.388 Fit side-chains REVERT: A 52 SER cc_start: 0.6702 (m) cc_final: 0.6393 (m) REVERT: A 53 ARG cc_start: 0.7789 (ttm110) cc_final: 0.7512 (mtt-85) REVERT: A 103 ARG cc_start: 0.7632 (tpp-160) cc_final: 0.7371 (ttp80) REVERT: B 52 SER cc_start: 0.6658 (OUTLIER) cc_final: 0.6165 (m) REVERT: B 53 ARG cc_start: 0.7728 (ttm110) cc_final: 0.7440 (mtt-85) REVERT: B 101 GLU cc_start: 0.5603 (OUTLIER) cc_final: 0.5385 (tm-30) REVERT: B 103 ARG cc_start: 0.7648 (tpp-160) cc_final: 0.7392 (ttp80) REVERT: C 52 SER cc_start: 0.6731 (OUTLIER) cc_final: 0.6246 (m) REVERT: C 53 ARG cc_start: 0.7908 (mtt90) cc_final: 0.7605 (mtt-85) REVERT: C 103 ARG cc_start: 0.7624 (tpp-160) cc_final: 0.7369 (ttp80) REVERT: D 52 SER cc_start: 0.6688 (m) cc_final: 0.6380 (m) REVERT: D 53 ARG cc_start: 0.7802 (ttm110) cc_final: 0.7480 (mtt-85) REVERT: D 103 ARG cc_start: 0.7639 (tpp-160) cc_final: 0.7378 (ttp80) outliers start: 19 outliers final: 7 residues processed: 66 average time/residue: 1.5052 time to fit residues: 102.0859 Evaluate side-chains 51 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 41 time to evaluate : 0.394 ------------------------------------------------------------------------------- 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 B residue 101 GLU 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 12 optimal weight: 8.9990 chunk 37 optimal weight: 5.9990 chunk 32 optimal weight: 5.9990 chunk 21 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 chunk 23 optimal weight: 9.9990 chunk 30 optimal weight: 5.9990 chunk 3 optimal weight: 9.9990 chunk 35 optimal weight: 0.9990 chunk 15 optimal weight: 3.9990 chunk 11 optimal weight: 5.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.172482 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.140901 restraints weight = 3024.248| |-----------------------------------------------------------------------------| r_work (start): 0.3617 rms_B_bonded: 1.39 r_work: 0.3472 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.3344 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.3344 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 moved from start: 0.2512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 3636 Z= 0.255 Angle : 0.828 6.981 4976 Z= 0.442 Chirality : 0.046 0.172 556 Planarity : 0.004 0.038 624 Dihedral : 8.725 61.011 512 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.85 % Allowed : 4.27 % Favored : 94.87 % Rotamer: Outliers : 4.94 % Allowed : 14.53 % Favored : 80.52 % 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: -0.89 (0.34), residues: 468 helix: -4.75 (0.27), residues: 24 sheet: 0.41 (0.26), residues: 288 loop : -1.77 (0.42), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.003 TRP D 79 HIS 0.001 0.001 HIS A 87 PHE 0.010 0.003 PHE A 29 TYR 0.008 0.002 TYR B 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 66 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 49 time to evaluate : 0.377 Fit side-chains REVERT: A 52 SER cc_start: 0.6774 (m) cc_final: 0.6419 (m) REVERT: A 53 ARG cc_start: 0.7790 (ttm110) cc_final: 0.7498 (mtt-85) REVERT: B 52 SER cc_start: 0.6755 (OUTLIER) cc_final: 0.6280 (m) REVERT: C 52 SER cc_start: 0.6793 (OUTLIER) cc_final: 0.6316 (m) REVERT: C 53 ARG cc_start: 0.7885 (mtt90) cc_final: 0.7467 (mtm-85) REVERT: D 52 SER cc_start: 0.6772 (m) cc_final: 0.6417 (m) outliers start: 17 outliers final: 8 residues processed: 63 average time/residue: 1.3046 time to fit residues: 84.6523 Evaluate side-chains 53 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 43 time to evaluate : 0.389 ------------------------------------------------------------------------------- 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 38 optimal weight: 20.0000 chunk 20 optimal weight: 10.0000 chunk 18 optimal weight: 6.9990 chunk 22 optimal weight: 20.0000 chunk 5 optimal weight: 20.0000 chunk 35 optimal weight: 0.5980 chunk 21 optimal weight: 0.0980 chunk 3 optimal weight: 0.1980 chunk 40 optimal weight: 7.9990 chunk 1 optimal weight: 2.9990 chunk 0 optimal weight: 5.9990 overall best weight: 1.9784 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.175106 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.143135 restraints weight = 3064.895| |-----------------------------------------------------------------------------| r_work (start): 0.3644 rms_B_bonded: 1.43 r_work: 0.3504 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.3376 rms_B_bonded: 3.34 restraints_weight: 0.2500 r_work (final): 0.3376 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 moved from start: 0.2840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 3636 Z= 0.186 Angle : 0.753 6.581 4976 Z= 0.402 Chirality : 0.044 0.161 556 Planarity : 0.004 0.030 624 Dihedral : 8.008 56.737 512 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.85 % Allowed : 4.27 % Favored : 94.87 % Rotamer: Outliers : 4.65 % Allowed : 15.70 % Favored : 79.65 % 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: -0.78 (0.34), residues: 468 helix: -4.95 (0.20), residues: 24 sheet: 0.46 (0.26), residues: 288 loop : -1.58 (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 0.009 0.002 PHE D 29 TYR 0.009 0.001 TYR B 96 ARG 0.004 0.001 ARG B 103 *********************** 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 66 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 50 time to evaluate : 0.357 Fit side-chains REVERT: A 52 SER cc_start: 0.6817 (m) cc_final: 0.6415 (m) REVERT: A 53 ARG cc_start: 0.7723 (ttm110) cc_final: 0.7431 (mtt-85) REVERT: B 52 SER cc_start: 0.6805 (OUTLIER) cc_final: 0.6335 (m) REVERT: C 52 SER cc_start: 0.6902 (OUTLIER) cc_final: 0.6433 (m) REVERT: C 53 ARG cc_start: 0.7830 (mtt90) cc_final: 0.7438 (mtm-85) REVERT: C 88 SER cc_start: 0.8879 (p) cc_final: 0.8656 (m) REVERT: D 52 SER cc_start: 0.6807 (m) cc_final: 0.6402 (m) REVERT: D 53 ARG cc_start: 0.7658 (ttm110) cc_final: 0.7366 (mtt-85) REVERT: D 88 SER cc_start: 0.8886 (p) cc_final: 0.8657 (m) outliers start: 16 outliers final: 11 residues processed: 63 average time/residue: 1.2645 time to fit residues: 82.1588 Evaluate side-chains 59 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 46 time to evaluate : 0.427 ------------------------------------------------------------------------------- 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 B residue 62 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 62 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 62 SER 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 4 optimal weight: 0.6980 chunk 41 optimal weight: 6.9990 chunk 15 optimal weight: 7.9990 chunk 22 optimal weight: 20.0000 chunk 12 optimal weight: 7.9990 chunk 16 optimal weight: 9.9990 chunk 26 optimal weight: 3.9990 chunk 24 optimal weight: 6.9990 chunk 23 optimal weight: 2.9990 chunk 25 optimal weight: 10.0000 chunk 27 optimal weight: 9.9990 overall best weight: 4.3388 ------------------------------------------------------------------------------- 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 = 0.3951 r_free = 0.3951 target = 0.170313 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.137654 restraints weight = 3074.363| |-----------------------------------------------------------------------------| r_work (start): 0.3567 rms_B_bonded: 1.46 r_work: 0.3428 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3303 rms_B_bonded: 3.36 restraints_weight: 0.2500 r_work (final): 0.3303 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8394 moved from start: 0.3115 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= 0.304 Angle : 0.839 7.233 4976 Z= 0.454 Chirality : 0.048 0.159 556 Planarity : 0.005 0.039 624 Dihedral : 8.318 55.837 512 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 10.19 Ramachandran Plot: Outliers : 0.85 % Allowed : 5.13 % Favored : 94.02 % Rotamer: Outliers : 7.27 % Allowed : 15.70 % Favored : 77.03 % 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: -0.95 (0.33), residues: 468 helix: -4.84 (0.22), residues: 24 sheet: 0.43 (0.26), residues: 288 loop : -1.92 (0.40), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.003 TRP A 79 HIS 0.002 0.001 HIS D 87 PHE 0.009 0.002 PHE D 29 TYR 0.009 0.002 TYR B 96 ARG 0.003 0.001 ARG A 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 73 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 48 time to evaluate : 0.357 Fit side-chains REVERT: A 52 SER cc_start: 0.6748 (m) cc_final: 0.6334 (m) REVERT: B 52 SER cc_start: 0.6779 (OUTLIER) cc_final: 0.6285 (m) REVERT: C 52 SER cc_start: 0.6858 (OUTLIER) cc_final: 0.6367 (m) REVERT: C 53 ARG cc_start: 0.7859 (mtt90) cc_final: 0.7523 (mtt-85) REVERT: D 52 SER cc_start: 0.6801 (m) cc_final: 0.6383 (m) outliers start: 25 outliers final: 12 residues processed: 66 average time/residue: 1.1603 time to fit residues: 79.1799 Evaluate side-chains 61 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 47 time to evaluate : 0.415 ------------------------------------------------------------------------------- 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 62 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 62 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 62 SER 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 17 optimal weight: 10.0000 chunk 6 optimal weight: 9.9990 chunk 13 optimal weight: 9.9990 chunk 3 optimal weight: 0.3980 chunk 5 optimal weight: 6.9990 chunk 8 optimal weight: 5.9990 chunk 4 optimal weight: 1.9990 chunk 40 optimal weight: 30.0000 chunk 24 optimal weight: 10.0000 chunk 15 optimal weight: 0.9980 chunk 43 optimal weight: 7.9990 overall best weight: 3.2786 ------------------------------------------------------------------------------- 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 = 0.3957 r_free = 0.3957 target = 0.170312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.138289 restraints weight = 3077.039| |-----------------------------------------------------------------------------| r_work (start): 0.3573 rms_B_bonded: 1.45 r_work: 0.3426 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.3304 rms_B_bonded: 3.35 restraints_weight: 0.2500 r_work (final): 0.3304 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8399 moved from start: 0.3223 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 : 0.789 7.210 4976 Z= 0.424 Chirality : 0.046 0.143 556 Planarity : 0.004 0.039 624 Dihedral : 7.750 49.405 512 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 1.71 % Allowed : 4.27 % Favored : 94.02 % Rotamer: Outliers : 4.65 % Allowed : 18.31 % Favored : 77.03 % 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: -0.82 (0.34), residues: 468 helix: -4.92 (0.20), residues: 24 sheet: 0.49 (0.26), residues: 288 loop : -1.75 (0.42), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.003 TRP A 79 HIS 0.001 0.001 HIS A 87 PHE 0.010 0.003 PHE D 29 TYR 0.010 0.002 TYR C 96 ARG 0.004 0.001 ARG D 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 63 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 47 time to evaluate : 0.353 Fit side-chains REVERT: A 52 SER cc_start: 0.6862 (m) cc_final: 0.6438 (m) REVERT: B 52 SER cc_start: 0.6801 (OUTLIER) cc_final: 0.6285 (m) REVERT: C 52 SER cc_start: 0.6903 (OUTLIER) cc_final: 0.6397 (m) REVERT: C 53 ARG cc_start: 0.7771 (mtt90) cc_final: 0.7463 (mtt-85) REVERT: D 52 SER cc_start: 0.6817 (m) cc_final: 0.6396 (m) outliers start: 16 outliers final: 10 residues processed: 56 average time/residue: 1.3791 time to fit residues: 79.4064 Evaluate side-chains 59 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 47 time to evaluate : 0.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 47 VAL 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 28 optimal weight: 6.9990 chunk 25 optimal weight: 5.9990 chunk 7 optimal weight: 7.9990 chunk 41 optimal weight: 0.9980 chunk 32 optimal weight: 8.9990 chunk 5 optimal weight: 7.9990 chunk 19 optimal weight: 5.9990 chunk 31 optimal weight: 3.9990 chunk 26 optimal weight: 0.9990 chunk 11 optimal weight: 10.0000 chunk 10 optimal weight: 0.0020 overall best weight: 2.3994 ------------------------------------------------------------------------------- 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 = 0.3974 r_free = 0.3974 target = 0.171197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.139440 restraints weight = 2997.638| |-----------------------------------------------------------------------------| r_work (start): 0.3592 rms_B_bonded: 1.43 r_work: 0.3447 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.3322 rms_B_bonded: 3.34 restraints_weight: 0.2500 r_work (final): 0.3322 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 moved from start: 0.3266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3636 Z= 0.211 Angle : 0.742 6.847 4976 Z= 0.398 Chirality : 0.045 0.143 556 Planarity : 0.003 0.033 624 Dihedral : 6.789 32.618 512 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.85 % Allowed : 5.98 % Favored : 93.16 % Rotamer: Outliers : 3.20 % Allowed : 18.90 % Favored : 77.91 % 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: -0.74 (0.34), residues: 468 helix: -4.97 (0.18), residues: 24 sheet: 0.53 (0.26), residues: 288 loop : -1.64 (0.43), 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 0.009 0.002 PHE D 29 TYR 0.011 0.001 TYR A 96 ARG 0.002 0.001 ARG D 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 63 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 52 time to evaluate : 0.291 Fit side-chains REVERT: A 52 SER cc_start: 0.6815 (m) cc_final: 0.6376 (m) REVERT: B 52 SER cc_start: 0.6771 (OUTLIER) cc_final: 0.6249 (m) REVERT: C 52 SER cc_start: 0.6832 (OUTLIER) cc_final: 0.6338 (m) REVERT: C 53 ARG cc_start: 0.7742 (mtt90) cc_final: 0.7446 (mtt-85) REVERT: D 52 SER cc_start: 0.6794 (m) cc_final: 0.6368 (m) outliers start: 11 outliers final: 9 residues processed: 60 average time/residue: 1.2646 time to fit residues: 78.1458 Evaluate side-chains 59 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 48 time to evaluate : 0.370 ------------------------------------------------------------------------------- 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 1 optimal weight: 9.9990 chunk 34 optimal weight: 9.9990 chunk 19 optimal weight: 9.9990 chunk 35 optimal weight: 5.9990 chunk 40 optimal weight: 9.9990 chunk 13 optimal weight: 10.0000 chunk 16 optimal weight: 7.9990 chunk 12 optimal weight: 4.9990 chunk 22 optimal weight: 20.0000 chunk 6 optimal weight: 10.0000 chunk 17 optimal weight: 10.0000 overall best weight: 7.7990 ------------------------------------------------------------------------------- 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 = 0.3929 r_free = 0.3929 target = 0.167709 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.135501 restraints weight = 3034.024| |-----------------------------------------------------------------------------| r_work (start): 0.3537 rms_B_bonded: 1.45 r_work: 0.3386 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3261 rms_B_bonded: 3.38 restraints_weight: 0.2500 r_work (final): 0.3261 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8434 moved from start: 0.3501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.052 3636 Z= 0.473 Angle : 0.941 7.919 4976 Z= 0.504 Chirality : 0.055 0.162 556 Planarity : 0.006 0.048 624 Dihedral : 7.469 24.127 512 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.85 % Allowed : 5.98 % Favored : 93.16 % Rotamer: Outliers : 4.36 % Allowed : 17.44 % Favored : 78.20 % 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: -1.09 (0.33), residues: 468 helix: -4.62 (0.29), residues: 24 sheet: 0.43 (0.25), residues: 288 loop : -2.27 (0.38), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.004 TRP D 120 HIS 0.003 0.001 HIS C 87 PHE 0.012 0.003 PHE D 29 TYR 0.013 0.003 TYR B 22 ARG 0.003 0.001 ARG D 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 57 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 42 time to evaluate : 0.395 Fit side-chains REVERT: B 52 SER cc_start: 0.6760 (OUTLIER) cc_final: 0.6176 (m) REVERT: C 52 SER cc_start: 0.6823 (OUTLIER) cc_final: 0.6268 (m) REVERT: C 53 ARG cc_start: 0.7816 (mtt90) cc_final: 0.7495 (mtt-85) outliers start: 15 outliers final: 11 residues processed: 55 average time/residue: 1.3558 time to fit residues: 76.7416 Evaluate side-chains 55 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 42 time to evaluate : 0.401 ------------------------------------------------------------------------------- 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 28 THR 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 41 optimal weight: 0.9990 chunk 5 optimal weight: 7.9990 chunk 15 optimal weight: 6.9990 chunk 0 optimal weight: 20.0000 chunk 32 optimal weight: 3.9990 chunk 43 optimal weight: 0.9990 chunk 25 optimal weight: 1.9990 chunk 40 optimal weight: 9.9990 chunk 12 optimal weight: 8.9990 chunk 6 optimal weight: 1.9990 chunk 20 optimal weight: 10.0000 overall best weight: 1.9990 ------------------------------------------------------------------------------- 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 = 0.3967 r_free = 0.3967 target = 0.170847 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.138625 restraints weight = 2986.463| |-----------------------------------------------------------------------------| r_work (start): 0.3586 rms_B_bonded: 1.46 r_work: 0.3448 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.3325 rms_B_bonded: 3.35 restraints_weight: 0.2500 r_work (final): 0.3325 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8377 moved from start: 0.3391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3636 Z= 0.195 Angle : 0.736 6.567 4976 Z= 0.395 Chirality : 0.045 0.135 556 Planarity : 0.003 0.030 624 Dihedral : 6.649 23.997 512 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.85 % Allowed : 4.70 % Favored : 94.44 % Rotamer: Outliers : 4.36 % Allowed : 18.31 % Favored : 77.33 % 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: -0.82 (0.34), residues: 468 helix: -4.80 (0.24), residues: 24 sheet: 0.51 (0.26), residues: 288 loop : -1.82 (0.43), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 79 HIS 0.001 0.000 HIS D 87 PHE 0.008 0.002 PHE C 29 TYR 0.011 0.001 TYR B 96 ARG 0.003 0.001 ARG A 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 59 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 44 time to evaluate : 0.375 Fit side-chains REVERT: B 52 SER cc_start: 0.6749 (OUTLIER) cc_final: 0.6210 (m) REVERT: C 52 SER cc_start: 0.6755 (OUTLIER) cc_final: 0.6249 (m) REVERT: C 53 ARG cc_start: 0.7751 (mtt90) cc_final: 0.7359 (mtm-85) outliers start: 15 outliers final: 5 residues processed: 52 average time/residue: 1.4738 time to fit residues: 78.6976 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 : 0.364 ------------------------------------------------------------------------------- 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 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 37 optimal weight: 10.0000 chunk 43 optimal weight: 4.9990 chunk 16 optimal weight: 10.0000 chunk 36 optimal weight: 10.0000 chunk 24 optimal weight: 9.9990 chunk 1 optimal weight: 0.4980 chunk 10 optimal weight: 0.5980 chunk 3 optimal weight: 10.0000 chunk 31 optimal weight: 10.0000 chunk 0 optimal weight: 9.9990 chunk 12 optimal weight: 0.3980 overall best weight: 3.2984 ------------------------------------------------------------------------------- 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 = 0.3955 r_free = 0.3955 target = 0.169706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.138221 restraints weight = 3005.748| |-----------------------------------------------------------------------------| r_work (start): 0.3577 rms_B_bonded: 1.42 r_work: 0.3430 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3306 rms_B_bonded: 3.36 restraints_weight: 0.2500 r_work (final): 0.3306 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8398 moved from start: 0.3420 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= 0.256 Angle : 0.786 7.190 4976 Z= 0.420 Chirality : 0.047 0.141 556 Planarity : 0.004 0.034 624 Dihedral : 6.825 23.739 512 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.85 % Allowed : 5.77 % Favored : 93.38 % Rotamer: Outliers : 2.62 % Allowed : 20.64 % 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: -0.83 (0.34), residues: 468 helix: -4.78 (0.24), residues: 24 sheet: 0.53 (0.26), residues: 288 loop : -1.91 (0.42), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.003 TRP D 108 HIS 0.001 0.001 HIS C 87 PHE 0.009 0.002 PHE C 29 TYR 0.013 0.002 TYR A 22 ARG 0.003 0.001 ARG A 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 53 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 44 time to evaluate : 0.413 Fit side-chains REVERT: B 52 SER cc_start: 0.6748 (OUTLIER) cc_final: 0.6202 (m) REVERT: C 52 SER cc_start: 0.6801 (OUTLIER) cc_final: 0.6271 (m) REVERT: C 53 ARG cc_start: 0.7779 (mtt90) cc_final: 0.7387 (mtm-85) outliers start: 9 outliers final: 6 residues processed: 48 average time/residue: 1.5731 time to fit residues: 77.4917 Evaluate side-chains 52 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 44 time to evaluate : 0.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain B residue 28 THR 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 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 6 optimal weight: 2.9990 chunk 26 optimal weight: 6.9990 chunk 10 optimal weight: 2.9990 chunk 22 optimal weight: 20.0000 chunk 33 optimal weight: 20.0000 chunk 32 optimal weight: 5.9990 chunk 14 optimal weight: 0.7980 chunk 23 optimal weight: 6.9990 chunk 17 optimal weight: 1.9990 chunk 38 optimal weight: 9.9990 chunk 9 optimal weight: 7.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- 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 = 0.3959 r_free = 0.3959 target = 0.169985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.138564 restraints weight = 3016.190| |-----------------------------------------------------------------------------| r_work (start): 0.3582 rms_B_bonded: 1.43 r_work: 0.3436 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3312 rms_B_bonded: 3.34 restraints_weight: 0.2500 r_work (final): 0.3312 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8394 moved from start: 0.3427 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= 0.240 Angle : 0.778 7.033 4976 Z= 0.415 Chirality : 0.046 0.138 556 Planarity : 0.004 0.033 624 Dihedral : 6.766 25.709 512 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.85 % Allowed : 5.34 % Favored : 93.80 % Rotamer: Outliers : 2.62 % Allowed : 20.93 % Favored : 76.45 % 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: -0.81 (0.34), residues: 468 helix: -4.81 (0.24), residues: 24 sheet: 0.54 (0.26), residues: 288 loop : -1.87 (0.43), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.003 TRP D 108 HIS 0.001 0.001 HIS D 87 PHE 0.009 0.002 PHE C 29 TYR 0.012 0.002 TYR A 22 ARG 0.003 0.001 ARG D 84 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3217.46 seconds wall clock time: 57 minutes 18.79 seconds (3438.79 seconds total)