Starting phenix.real_space_refine on Fri Aug 22 13:41:44 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8gvk_32099/08_2025/8gvk_32099.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gvk_32099/08_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 { model { file = "/net/cci-nas-00/data/ceres_data/8gvk_32099/08_2025/8gvk_32099.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gvk_32099/08_2025/8gvk_32099.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8gvk_32099/08_2025/8gvk_32099.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gvk_32099/08_2025/8gvk_32099.map" } resolution = 2.2 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 0.85, per 1000 atoms: 0.24 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: 0.23 Conformation dependent library (CDL) restraints added in 116.8 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.16 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: 0.54 Time building geometry restraints manager: 0.33 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: 0.01 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: 0.490 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: 0.000 Extract box with map and model: 0.080 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 4.670 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 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:7.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.630 ------------------------------------------------------------------------------- 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= 0.323 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.002 0.000 ARG C 84 TYR 0.010 0.002 TYR A 96 PHE 0.011 0.002 PHE C 29 TRP 0.013 0.003 TRP B 108 HIS 0.001 0.000 HIS C 87 Details of bonding type rmsd covalent geometry : bond 0.00639 ( 3636) covalent geometry : angle 1.28943 ( 4976) hydrogen bonds : bond 0.20417 ( 192) hydrogen bonds : angle 8.99974 ( 516) *********************** 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 : 0.123 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: 0.5680 time to fit residues: 41.2956 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 : 0.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 24 optimal weight: 3.9990 chunk 26 optimal weight: 6.9990 chunk 2 optimal weight: 6.9990 chunk 16 optimal weight: 10.0000 chunk 32 optimal weight: 6.9990 chunk 31 optimal weight: 7.9990 chunk 25 optimal weight: 5.9990 chunk 19 optimal weight: 3.9990 chunk 30 optimal weight: 5.9990 chunk 22 optimal weight: 10.0000 chunk 37 optimal weight: 4.9990 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 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 = 0.3974 r_free = 0.3974 target = 0.171791 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.140146 restraints weight = 3103.591| |-----------------------------------------------------------------------------| r_work (start): 0.3606 rms_B_bonded: 1.41 r_work: 0.3458 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3334 rms_B_bonded: 3.43 restraints_weight: 0.2500 r_work (final): 0.3334 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8376 moved from start: 0.2181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 3636 Z= 0.275 Angle : 0.929 7.675 4976 Z= 0.498 Chirality : 0.050 0.164 556 Planarity : 0.005 0.044 624 Dihedral : 9.593 67.136 512 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 2.56 % Allowed : 4.27 % Favored : 93.16 % Rotamer: Outliers : 5.52 % Allowed : 10.76 % Favored : 83.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 1.71 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.63 (0.34), residues: 468 helix: None (None), residues: 0 sheet: 0.07 (0.25), residues: 284 loop : -1.09 (0.42), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 84 TYR 0.010 0.002 TYR D 83 PHE 0.014 0.003 PHE A 29 TRP 0.015 0.003 TRP D 79 HIS 0.002 0.001 HIS D 87 Details of bonding type rmsd covalent geometry : bond 0.00534 ( 3636) covalent geometry : angle 0.92888 ( 4976) hydrogen bonds : bond 0.05443 ( 192) hydrogen bonds : angle 7.49322 ( 516) *********************** 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 : 0.146 Fit side-chains REVERT: A 52 SER cc_start: 0.6691 (m) cc_final: 0.6362 (m) REVERT: A 53 ARG cc_start: 0.7767 (ttm110) cc_final: 0.7478 (mtt-85) REVERT: A 103 ARG cc_start: 0.7623 (tpp-160) cc_final: 0.7358 (ttp80) REVERT: B 52 SER cc_start: 0.6679 (OUTLIER) cc_final: 0.6177 (m) REVERT: B 53 ARG cc_start: 0.7705 (ttm110) cc_final: 0.7420 (mtt-85) REVERT: B 103 ARG cc_start: 0.7635 (tpp-160) cc_final: 0.7380 (ttp80) REVERT: C 52 SER cc_start: 0.6745 (OUTLIER) cc_final: 0.6244 (m) REVERT: C 53 ARG cc_start: 0.7887 (mtt90) cc_final: 0.7575 (mtt-85) REVERT: C 103 ARG cc_start: 0.7609 (tpp-160) cc_final: 0.7380 (ttp80) REVERT: D 52 SER cc_start: 0.6684 (m) cc_final: 0.6354 (m) REVERT: D 53 ARG cc_start: 0.7779 (ttm110) cc_final: 0.7448 (mtt-85) REVERT: D 103 ARG cc_start: 0.7632 (tpp-160) cc_final: 0.7391 (ttp80) outliers start: 19 outliers final: 7 residues processed: 66 average time/residue: 0.7564 time to fit residues: 51.1232 Evaluate side-chains 51 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 42 time to evaluate : 0.133 ------------------------------------------------------------------------------- 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 40 optimal weight: 10.0000 chunk 39 optimal weight: 0.6980 chunk 27 optimal weight: 9.9990 chunk 38 optimal weight: 7.9990 chunk 25 optimal weight: 10.0000 chunk 41 optimal weight: 6.9990 chunk 16 optimal weight: 10.0000 chunk 43 optimal weight: 5.9990 chunk 30 optimal weight: 4.9990 chunk 1 optimal weight: 0.9980 chunk 22 optimal weight: 9.9990 overall best weight: 3.9386 ------------------------------------------------------------------------------- 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 = 0.3981 r_free = 0.3981 target = 0.171982 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.139505 restraints weight = 3043.884| |-----------------------------------------------------------------------------| r_work (start): 0.3602 rms_B_bonded: 1.43 r_work: 0.3458 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3329 rms_B_bonded: 3.35 restraints_weight: 0.2500 r_work (final): 0.3329 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8376 moved from start: 0.2538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 3636 Z= 0.232 Angle : 0.868 7.291 4976 Z= 0.464 Chirality : 0.048 0.178 556 Planarity : 0.005 0.041 624 Dihedral : 8.888 61.550 512 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.85 % Allowed : 4.49 % Favored : 94.66 % Rotamer: Outliers : 4.94 % Allowed : 15.41 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.04 (0.33), residues: 468 helix: -4.64 (0.32), residues: 24 sheet: 0.34 (0.26), residues: 284 loop : -1.90 (0.40), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 84 TYR 0.008 0.002 TYR A 96 PHE 0.011 0.003 PHE A 29 TRP 0.012 0.003 TRP D 79 HIS 0.001 0.001 HIS C 87 Details of bonding type rmsd covalent geometry : bond 0.00448 ( 3636) covalent geometry : angle 0.86817 ( 4976) hydrogen bonds : bond 0.04907 ( 192) hydrogen bonds : angle 7.48724 ( 516) *********************** 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 60 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 43 time to evaluate : 0.160 Fit side-chains REVERT: A 52 SER cc_start: 0.6755 (m) cc_final: 0.6378 (m) REVERT: A 103 ARG cc_start: 0.7512 (tpp-160) cc_final: 0.7294 (ttp80) REVERT: B 52 SER cc_start: 0.6737 (OUTLIER) cc_final: 0.6245 (m) REVERT: B 103 ARG cc_start: 0.7511 (tpp-160) cc_final: 0.7310 (ttp80) REVERT: C 52 SER cc_start: 0.6791 (OUTLIER) cc_final: 0.6306 (m) REVERT: C 53 ARG cc_start: 0.7886 (mtt90) cc_final: 0.7452 (mtm-85) REVERT: D 52 SER cc_start: 0.6720 (m) cc_final: 0.6350 (m) outliers start: 17 outliers final: 8 residues processed: 57 average time/residue: 0.7188 time to fit residues: 42.0091 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 : 0.136 ------------------------------------------------------------------------------- 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 3 optimal weight: 10.0000 chunk 22 optimal weight: 20.0000 chunk 10 optimal weight: 0.9990 chunk 26 optimal weight: 9.9990 chunk 5 optimal weight: 10.0000 chunk 42 optimal weight: 10.0000 chunk 27 optimal weight: 7.9990 chunk 35 optimal weight: 9.9990 chunk 9 optimal weight: 3.9990 chunk 29 optimal weight: 3.9990 chunk 30 optimal weight: 0.9980 overall best weight: 3.5988 ------------------------------------------------------------------------------- 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 = 0.3976 r_free = 0.3976 target = 0.172159 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.140810 restraints weight = 3044.122| |-----------------------------------------------------------------------------| r_work (start): 0.3606 rms_B_bonded: 1.40 r_work: 0.3463 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.3336 rms_B_bonded: 3.33 restraints_weight: 0.2500 r_work (final): 0.3336 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 moved from start: 0.2886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 3636 Z= 0.216 Angle : 0.845 7.363 4976 Z= 0.450 Chirality : 0.047 0.170 556 Planarity : 0.005 0.038 624 Dihedral : 8.468 58.438 512 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.85 % Allowed : 4.91 % Favored : 94.23 % Rotamer: Outliers : 5.23 % Allowed : 15.70 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.03 (0.34), residues: 468 helix: -4.81 (0.24), residues: 24 sheet: 0.38 (0.26), residues: 284 loop : -1.94 (0.40), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG D 103 TYR 0.010 0.002 TYR C 96 PHE 0.010 0.003 PHE A 29 TRP 0.011 0.003 TRP A 79 HIS 0.001 0.001 HIS D 87 Details of bonding type rmsd covalent geometry : bond 0.00419 ( 3636) covalent geometry : angle 0.84500 ( 4976) hydrogen bonds : bond 0.04689 ( 192) hydrogen bonds : angle 7.43559 ( 516) *********************** 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 62 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 44 time to evaluate : 0.213 Fit side-chains REVERT: A 52 SER cc_start: 0.6811 (m) cc_final: 0.6414 (m) REVERT: B 52 SER cc_start: 0.6819 (OUTLIER) cc_final: 0.6339 (m) REVERT: B 103 ARG cc_start: 0.7503 (tpp-160) cc_final: 0.7303 (ttp80) REVERT: C 52 SER cc_start: 0.6828 (OUTLIER) cc_final: 0.6349 (m) REVERT: C 53 ARG cc_start: 0.7888 (mtt90) cc_final: 0.7579 (mtt-85) REVERT: D 52 SER cc_start: 0.6778 (m) cc_final: 0.6395 (m) REVERT: D 53 ARG cc_start: 0.7804 (ttm110) cc_final: 0.7512 (mtt-85) outliers start: 18 outliers final: 8 residues processed: 58 average time/residue: 0.7240 time to fit residues: 43.1070 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 : 0.136 ------------------------------------------------------------------------------- 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 13 optimal weight: 5.9990 chunk 30 optimal weight: 0.3980 chunk 35 optimal weight: 6.9990 chunk 4 optimal weight: 3.9990 chunk 37 optimal weight: 0.9980 chunk 12 optimal weight: 7.9990 chunk 19 optimal weight: 5.9990 chunk 1 optimal weight: 5.9990 chunk 14 optimal weight: 0.5980 chunk 31 optimal weight: 9.9990 chunk 40 optimal weight: 0.5980 overall best weight: 1.3182 ------------------------------------------------------------------------------- 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 = 0.4032 r_free = 0.4032 target = 0.176498 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.145495 restraints weight = 3032.608| |-----------------------------------------------------------------------------| r_work (start): 0.3677 rms_B_bonded: 1.40 r_work: 0.3538 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.3411 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.3411 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8308 moved from start: 0.2975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 3636 Z= 0.131 Angle : 0.713 5.911 4976 Z= 0.381 Chirality : 0.043 0.146 556 Planarity : 0.003 0.026 624 Dihedral : 7.437 51.042 512 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.85 % Allowed : 4.27 % Favored : 94.87 % Rotamer: Outliers : 3.49 % Allowed : 18.90 % Favored : 77.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.85 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.88 (0.35), residues: 468 helix: -5.00 (0.18), residues: 24 sheet: 0.29 (0.27), residues: 292 loop : -1.45 (0.45), residues: 152 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 103 TYR 0.011 0.001 TYR A 96 PHE 0.008 0.002 PHE D 29 TRP 0.012 0.002 TRP D 108 HIS 0.000 0.000 HIS A 127 Details of bonding type rmsd covalent geometry : bond 0.00242 ( 3636) covalent geometry : angle 0.71272 ( 4976) hydrogen bonds : bond 0.04084 ( 192) hydrogen bonds : angle 7.11870 ( 516) *********************** 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 70 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 58 time to evaluate : 0.159 Fit side-chains REVERT: A 52 SER cc_start: 0.6796 (m) cc_final: 0.6386 (m) REVERT: A 53 ARG cc_start: 0.7706 (ttm110) cc_final: 0.7414 (mtt-85) REVERT: A 88 SER cc_start: 0.8845 (p) cc_final: 0.8640 (m) REVERT: B 52 SER cc_start: 0.6863 (OUTLIER) cc_final: 0.6559 (m) REVERT: C 52 SER cc_start: 0.6843 (OUTLIER) cc_final: 0.6382 (m) REVERT: C 53 ARG cc_start: 0.7821 (mtt90) cc_final: 0.7462 (mtm-85) REVERT: D 52 SER cc_start: 0.6811 (m) cc_final: 0.6399 (m) REVERT: D 53 ARG cc_start: 0.7705 (ttm110) cc_final: 0.7424 (mtt-85) outliers start: 12 outliers final: 4 residues processed: 67 average time/residue: 0.5762 time to fit residues: 39.8293 Evaluate side-chains 55 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 49 time to evaluate : 0.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 52 SER Chi-restraints excluded: chain B residue 62 SER Chi-restraints excluded: chain C residue 52 SER Chi-restraints excluded: chain C residue 62 SER Chi-restraints excluded: chain D residue 28 THR Chi-restraints excluded: chain D residue 62 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 18 optimal weight: 20.0000 chunk 34 optimal weight: 6.9990 chunk 25 optimal weight: 9.9990 chunk 24 optimal weight: 7.9990 chunk 1 optimal weight: 20.0000 chunk 33 optimal weight: 10.0000 chunk 2 optimal weight: 6.9990 chunk 37 optimal weight: 10.0000 chunk 32 optimal weight: 5.9990 chunk 16 optimal weight: 9.9990 chunk 14 optimal weight: 5.9990 overall best weight: 6.7990 ------------------------------------------------------------------------------- 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 = 0.3948 r_free = 0.3948 target = 0.169933 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.137998 restraints weight = 3026.311| |-----------------------------------------------------------------------------| r_work (start): 0.3566 rms_B_bonded: 1.42 r_work: 0.3420 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.3294 rms_B_bonded: 3.34 restraints_weight: 0.2500 r_work (final): 0.3294 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8409 moved from start: 0.3363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.046 3636 Z= 0.331 Angle : 0.935 7.787 4976 Z= 0.508 Chirality : 0.053 0.163 556 Planarity : 0.006 0.047 624 Dihedral : 8.130 46.243 512 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 1.71 % Allowed : 4.91 % Favored : 93.38 % Rotamer: Outliers : 5.81 % Allowed : 17.73 % Favored : 76.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.85 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.16 (0.33), residues: 468 helix: -4.55 (0.33), residues: 24 sheet: 0.37 (0.26), residues: 284 loop : -2.24 (0.38), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 103 TYR 0.011 0.003 TYR D 22 PHE 0.011 0.003 PHE D 29 TRP 0.015 0.004 TRP A 120 HIS 0.002 0.001 HIS B 87 Details of bonding type rmsd covalent geometry : bond 0.00651 ( 3636) covalent geometry : angle 0.93516 ( 4976) hydrogen bonds : bond 0.05186 ( 192) hydrogen bonds : angle 7.68487 ( 516) *********************** 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 68 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 48 time to evaluate : 0.160 Fit side-chains REVERT: A 52 SER cc_start: 0.6745 (m) cc_final: 0.6292 (m) REVERT: B 52 SER cc_start: 0.6770 (OUTLIER) cc_final: 0.6244 (m) REVERT: C 52 SER cc_start: 0.6806 (OUTLIER) cc_final: 0.6285 (m) REVERT: C 53 ARG cc_start: 0.7880 (mtt90) cc_final: 0.7566 (mtt-85) REVERT: D 52 SER cc_start: 0.6743 (m) cc_final: 0.6291 (m) outliers start: 20 outliers final: 7 residues processed: 62 average time/residue: 0.6508 time to fit residues: 41.5068 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 : 0.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 52 SER Chi-restraints excluded: chain B residue 62 SER Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 52 SER Chi-restraints excluded: chain C residue 62 SER Chi-restraints excluded: chain D residue 28 THR Chi-restraints excluded: chain D residue 62 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 21 optimal weight: 0.7980 chunk 26 optimal weight: 8.9990 chunk 3 optimal weight: 0.9990 chunk 19 optimal weight: 4.9990 chunk 9 optimal weight: 0.9980 chunk 17 optimal weight: 0.0020 chunk 31 optimal weight: 5.9990 chunk 13 optimal weight: 9.9990 chunk 38 optimal weight: 9.9990 chunk 14 optimal weight: 5.9990 chunk 36 optimal weight: 8.9990 overall best weight: 1.5592 ------------------------------------------------------------------------------- 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 = 0.3988 r_free = 0.3988 target = 0.172996 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.141257 restraints weight = 3038.001| |-----------------------------------------------------------------------------| r_work (start): 0.3612 rms_B_bonded: 1.43 r_work: 0.3472 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.3351 rms_B_bonded: 3.34 restraints_weight: 0.2500 r_work (final): 0.3351 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 moved from start: 0.3333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 3636 Z= 0.143 Angle : 0.714 6.524 4976 Z= 0.384 Chirality : 0.044 0.136 556 Planarity : 0.003 0.026 624 Dihedral : 6.671 31.873 512 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.85 % Allowed : 4.27 % Favored : 94.87 % Rotamer: Outliers : 6.10 % Allowed : 17.44 % Favored : 76.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.43 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.72 (0.35), residues: 468 helix: -4.91 (0.20), residues: 24 sheet: 0.56 (0.26), residues: 288 loop : -1.68 (0.44), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 103 TYR 0.011 0.001 TYR B 96 PHE 0.008 0.002 PHE D 29 TRP 0.012 0.002 TRP D 79 HIS 0.001 0.000 HIS C 87 Details of bonding type rmsd covalent geometry : bond 0.00268 ( 3636) covalent geometry : angle 0.71430 ( 4976) hydrogen bonds : bond 0.04113 ( 192) hydrogen bonds : angle 7.10598 ( 516) *********************** 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 73 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 52 time to evaluate : 0.139 Fit side-chains REVERT: A 52 SER cc_start: 0.6831 (m) cc_final: 0.6397 (m) REVERT: A 88 SER cc_start: 0.8818 (p) cc_final: 0.8588 (m) REVERT: B 52 SER cc_start: 0.6835 (OUTLIER) cc_final: 0.6358 (m) REVERT: C 52 SER cc_start: 0.6833 (OUTLIER) cc_final: 0.6347 (m) REVERT: C 53 ARG cc_start: 0.7755 (mtt90) cc_final: 0.7474 (mtt-85) REVERT: D 52 SER cc_start: 0.6817 (m) cc_final: 0.6380 (m) outliers start: 21 outliers final: 5 residues processed: 64 average time/residue: 0.6440 time to fit residues: 42.4413 Evaluate side-chains 57 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 50 time to evaluate : 0.137 ------------------------------------------------------------------------------- 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 18 optimal weight: 9.9990 chunk 23 optimal weight: 5.9990 chunk 0 optimal weight: 20.0000 chunk 1 optimal weight: 5.9990 chunk 2 optimal weight: 9.9990 chunk 4 optimal weight: 0.9980 chunk 35 optimal weight: 9.9990 chunk 15 optimal weight: 5.9990 chunk 6 optimal weight: 10.0000 chunk 10 optimal weight: 0.8980 chunk 8 optimal weight: 7.9990 overall best weight: 3.9786 ------------------------------------------------------------------------------- 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 = 0.170024 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.137878 restraints weight = 3053.796| |-----------------------------------------------------------------------------| r_work (start): 0.3568 rms_B_bonded: 1.44 r_work: 0.3421 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3296 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.3296 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8405 moved from start: 0.3409 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= 0.226 Angle : 0.809 7.640 4976 Z= 0.432 Chirality : 0.048 0.144 556 Planarity : 0.004 0.039 624 Dihedral : 6.928 24.869 512 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.85 % Allowed : 5.98 % Favored : 93.16 % Rotamer: Outliers : 3.78 % Allowed : 21.51 % Favored : 74.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.82 (0.34), residues: 468 helix: -4.72 (0.27), residues: 24 sheet: 0.58 (0.26), residues: 288 loop : -2.00 (0.41), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG A 84 TYR 0.011 0.002 TYR A 22 PHE 0.009 0.002 PHE D 29 TRP 0.010 0.003 TRP D 108 HIS 0.001 0.001 HIS C 87 Details of bonding type rmsd covalent geometry : bond 0.00436 ( 3636) covalent geometry : angle 0.80895 ( 4976) hydrogen bonds : bond 0.04553 ( 192) hydrogen bonds : angle 7.42844 ( 516) *********************** 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 59 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 46 time to evaluate : 0.141 Fit side-chains REVERT: B 52 SER cc_start: 0.6731 (OUTLIER) cc_final: 0.6198 (m) REVERT: C 52 SER cc_start: 0.6784 (OUTLIER) cc_final: 0.6270 (m) REVERT: C 53 ARG cc_start: 0.7809 (mtt90) cc_final: 0.7480 (mtt-85) outliers start: 13 outliers final: 4 residues processed: 50 average time/residue: 0.7771 time to fit residues: 39.8036 Evaluate side-chains 52 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 46 time to evaluate : 0.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain B residue 28 THR 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 4 optimal weight: 4.9990 chunk 19 optimal weight: 7.9990 chunk 7 optimal weight: 7.9990 chunk 31 optimal weight: 6.9990 chunk 3 optimal weight: 7.9990 chunk 12 optimal weight: 20.0000 chunk 6 optimal weight: 5.9990 chunk 11 optimal weight: 10.0000 chunk 37 optimal weight: 6.9990 chunk 2 optimal weight: 0.9990 chunk 36 optimal weight: 5.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- 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 = 0.3943 r_free = 0.3943 target = 0.169089 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.137041 restraints weight = 2995.109| |-----------------------------------------------------------------------------| r_work (start): 0.3554 rms_B_bonded: 1.44 r_work: 0.3407 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3284 rms_B_bonded: 3.35 restraints_weight: 0.2500 r_work (final): 0.3284 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8414 moved from start: 0.3494 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= 0.261 Angle : 0.861 8.214 4976 Z= 0.457 Chirality : 0.050 0.151 556 Planarity : 0.005 0.042 624 Dihedral : 7.189 23.785 512 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.85 % Allowed : 5.98 % Favored : 93.16 % Rotamer: Outliers : 2.33 % Allowed : 22.97 % Favored : 74.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.91 (0.34), residues: 468 helix: -4.50 (0.35), residues: 24 sheet: 0.52 (0.26), residues: 288 loop : -2.10 (0.41), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG A 84 TYR 0.012 0.002 TYR A 22 PHE 0.010 0.003 PHE D 29 TRP 0.012 0.003 TRP B 120 HIS 0.002 0.001 HIS C 87 Details of bonding type rmsd covalent geometry : bond 0.00511 ( 3636) covalent geometry : angle 0.86101 ( 4976) hydrogen bonds : bond 0.04745 ( 192) hydrogen bonds : angle 7.55094 ( 516) *********************** 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 50 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 42 time to evaluate : 0.144 Fit side-chains REVERT: B 52 SER cc_start: 0.6687 (OUTLIER) cc_final: 0.6141 (m) REVERT: C 52 SER cc_start: 0.6814 (OUTLIER) cc_final: 0.6279 (m) REVERT: C 53 ARG cc_start: 0.7804 (mtt90) cc_final: 0.7398 (mtm-85) outliers start: 8 outliers final: 3 residues processed: 48 average time/residue: 0.8056 time to fit residues: 39.6094 Evaluate side-chains 47 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 42 time to evaluate : 0.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 52 SER Chi-restraints excluded: chain C residue 52 SER Chi-restraints excluded: chain D residue 28 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 40 optimal weight: 20.0000 chunk 30 optimal weight: 4.9990 chunk 20 optimal weight: 10.0000 chunk 36 optimal weight: 3.9990 chunk 4 optimal weight: 6.9990 chunk 3 optimal weight: 8.9990 chunk 18 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 0 optimal weight: 20.0000 chunk 24 optimal weight: 9.9990 chunk 15 optimal weight: 6.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- 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 = 0.3948 r_free = 0.3948 target = 0.169433 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.137370 restraints weight = 3046.504| |-----------------------------------------------------------------------------| r_work (start): 0.3558 rms_B_bonded: 1.44 r_work: 0.3412 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.3290 rms_B_bonded: 3.35 restraints_weight: 0.2500 r_work (final): 0.3290 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8408 moved from start: 0.3490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 3636 Z= 0.232 Angle : 0.838 7.976 4976 Z= 0.444 Chirality : 0.048 0.146 556 Planarity : 0.004 0.039 624 Dihedral : 7.104 24.851 512 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.85 % Allowed : 5.77 % Favored : 93.38 % Rotamer: Outliers : 1.74 % Allowed : 23.55 % Favored : 74.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.91 (0.34), residues: 468 helix: -4.47 (0.37), residues: 24 sheet: 0.50 (0.26), residues: 288 loop : -2.07 (0.41), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG D 84 TYR 0.012 0.002 TYR A 22 PHE 0.010 0.002 PHE D 29 TRP 0.010 0.003 TRP D 108 HIS 0.002 0.001 HIS B 87 Details of bonding type rmsd covalent geometry : bond 0.00454 ( 3636) covalent geometry : angle 0.83763 ( 4976) hydrogen bonds : bond 0.04585 ( 192) hydrogen bonds : angle 7.49172 ( 516) ********************** 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 47 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 41 time to evaluate : 0.138 Fit side-chains REVERT: B 52 SER cc_start: 0.6667 (OUTLIER) cc_final: 0.6126 (m) REVERT: C 52 SER cc_start: 0.6803 (OUTLIER) cc_final: 0.6264 (m) REVERT: C 53 ARG cc_start: 0.7776 (mtt90) cc_final: 0.7386 (mtm-85) outliers start: 6 outliers final: 1 residues processed: 46 average time/residue: 0.8139 time to fit residues: 38.3249 Evaluate side-chains 44 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 41 time to evaluate : 0.093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 52 SER Chi-restraints excluded: chain C residue 52 SER Chi-restraints excluded: chain D residue 28 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 27 optimal weight: 9.9990 chunk 33 optimal weight: 20.0000 chunk 28 optimal weight: 5.9990 chunk 18 optimal weight: 20.0000 chunk 37 optimal weight: 2.9990 chunk 23 optimal weight: 7.9990 chunk 39 optimal weight: 10.0000 chunk 17 optimal weight: 0.7980 chunk 32 optimal weight: 2.9990 chunk 29 optimal weight: 5.9990 chunk 10 optimal weight: 1.9990 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 = 0.3957 r_free = 0.3957 target = 0.170120 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.138602 restraints weight = 2980.256| |-----------------------------------------------------------------------------| r_work (start): 0.3579 rms_B_bonded: 1.41 r_work: 0.3434 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.3311 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.3311 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8392 moved from start: 0.3474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 3636 Z= 0.189 Angle : 0.790 7.415 4976 Z= 0.419 Chirality : 0.046 0.138 556 Planarity : 0.004 0.034 624 Dihedral : 6.884 26.803 512 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.85 % Allowed : 5.34 % Favored : 93.80 % Rotamer: Outliers : 1.74 % Allowed : 22.38 % Favored : 75.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.83 (0.34), residues: 468 helix: -4.61 (0.32), residues: 24 sheet: 0.54 (0.26), residues: 288 loop : -1.94 (0.43), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 84 TYR 0.011 0.002 TYR A 22 PHE 0.009 0.002 PHE D 29 TRP 0.011 0.003 TRP C 79 HIS 0.001 0.001 HIS D 87 Details of bonding type rmsd covalent geometry : bond 0.00367 ( 3636) covalent geometry : angle 0.79006 ( 4976) hydrogen bonds : bond 0.04327 ( 192) hydrogen bonds : angle 7.34900 ( 516) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1763.06 seconds wall clock time: 30 minutes 53.02 seconds (1853.02 seconds total)