Starting phenix.real_space_refine on Wed Mar 5 20:01:27 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8gvk_32099/03_2025/8gvk_32099.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gvk_32099/03_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_32099/03_2025/8gvk_32099.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gvk_32099/03_2025/8gvk_32099.map" model { file = "/net/cci-nas-00/data/ceres_data/8gvk_32099/03_2025/8gvk_32099.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gvk_32099/03_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-5624/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: 2.62, per 1000 atoms: 0.73 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: 0.74 Conformation dependent library (CDL) restraints added in 408.6 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: 0.50 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: 1.17 Time building geometry restraints manager: 0.89 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: 0.590 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: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 12.810 Find NCS groups from input model: 0.080 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:12.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.700 ------------------------------------------------------------------------------- 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 : 0.385 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: 1.3167 time to fit residues: 96.1303 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 : 0.291 ------------------------------------------------------------------------------- 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 = 0.171372 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.139868 restraints weight = 3066.433| |-----------------------------------------------------------------------------| r_work (start): 0.3599 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 67.033 512 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 : 0.347 Fit side-chains REVERT: A 52 SER cc_start: 0.6699 (m) cc_final: 0.6383 (m) REVERT: A 53 ARG cc_start: 0.7775 (ttm110) cc_final: 0.7487 (mtt-85) REVERT: A 103 ARG cc_start: 0.7628 (tpp-160) cc_final: 0.7367 (ttp80) REVERT: B 52 SER cc_start: 0.6659 (OUTLIER) cc_final: 0.6156 (m) REVERT: B 53 ARG cc_start: 0.7717 (ttm110) cc_final: 0.7419 (mtt-85) REVERT: B 101 GLU cc_start: 0.5573 (OUTLIER) cc_final: 0.5361 (tm-30) REVERT: B 103 ARG cc_start: 0.7644 (tpp-160) cc_final: 0.7390 (ttp80) REVERT: C 52 SER cc_start: 0.6728 (OUTLIER) cc_final: 0.6235 (m) REVERT: C 53 ARG cc_start: 0.7890 (mtt90) cc_final: 0.7583 (mtt-85) REVERT: C 103 ARG cc_start: 0.7618 (tpp-160) cc_final: 0.7365 (ttp80) REVERT: D 52 SER cc_start: 0.6683 (m) cc_final: 0.6368 (m) REVERT: D 53 ARG cc_start: 0.7790 (ttm110) cc_final: 0.7458 (mtt-85) REVERT: D 103 ARG cc_start: 0.7635 (tpp-160) cc_final: 0.7378 (ttp80) outliers start: 19 outliers final: 7 residues processed: 66 average time/residue: 1.3657 time to fit residues: 92.6281 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 : 0.350 ------------------------------------------------------------------------------- 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: 2.9990 chunk 41 optimal weight: 2.9990 chunk 23 optimal weight: 9.9990 chunk 30 optimal weight: 5.9990 chunk 3 optimal weight: 8.9990 chunk 35 optimal weight: 2.9990 chunk 15 optimal weight: 3.9990 chunk 11 optimal weight: 4.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- 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 = 0.3980 r_free = 0.3980 target = 0.171882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.140346 restraints weight = 3023.038| |-----------------------------------------------------------------------------| r_work (start): 0.3609 rms_B_bonded: 1.39 r_work: 0.3463 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.3334 rms_B_bonded: 3.34 restraints_weight: 0.2500 r_work (final): 0.3334 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8376 moved from start: 0.2540 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= 0.276 Angle : 0.848 7.119 4976 Z= 0.453 Chirality : 0.047 0.176 556 Planarity : 0.005 0.040 624 Dihedral : 8.849 61.573 512 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.85 % Allowed : 4.27 % Favored : 94.87 % Rotamer: Outliers : 4.94 % Allowed : 14.83 % Favored : 80.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.85 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.94 (0.34), residues: 468 helix: -4.70 (0.30), residues: 24 sheet: 0.39 (0.26), residues: 288 loop : -1.84 (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 B 87 PHE 0.011 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 63 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 46 time to evaluate : 0.367 Fit side-chains REVERT: A 52 SER cc_start: 0.6738 (m) cc_final: 0.6383 (m) REVERT: A 53 ARG cc_start: 0.7796 (ttm110) cc_final: 0.7509 (mtt-85) REVERT: B 52 SER cc_start: 0.6733 (OUTLIER) cc_final: 0.6250 (m) REVERT: C 52 SER cc_start: 0.6799 (OUTLIER) cc_final: 0.6321 (m) REVERT: C 53 ARG cc_start: 0.7883 (mtt90) cc_final: 0.7461 (mtm-85) REVERT: D 52 SER cc_start: 0.6757 (m) cc_final: 0.6399 (m) outliers start: 17 outliers final: 8 residues processed: 60 average time/residue: 1.2792 time to fit residues: 79.0037 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 : 0.345 ------------------------------------------------------------------------------- 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: 9.9990 chunk 18 optimal weight: 7.9990 chunk 22 optimal weight: 20.0000 chunk 5 optimal weight: 20.0000 chunk 35 optimal weight: 2.9990 chunk 21 optimal weight: 0.0670 chunk 3 optimal weight: 0.0670 chunk 40 optimal weight: 9.9990 chunk 1 optimal weight: 2.9990 chunk 0 optimal weight: 5.9990 overall best weight: 2.4262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 107 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.173908 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.142040 restraints weight = 3067.200| |-----------------------------------------------------------------------------| r_work (start): 0.3628 rms_B_bonded: 1.42 r_work: 0.3486 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.3360 rms_B_bonded: 3.33 restraints_weight: 0.2500 r_work (final): 0.3360 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8355 moved from start: 0.2858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3636 Z= 0.209 Angle : 0.782 6.876 4976 Z= 0.416 Chirality : 0.045 0.164 556 Planarity : 0.004 0.033 624 Dihedral : 8.197 57.591 512 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.85 % Allowed : 4.27 % Favored : 94.87 % Rotamer: Outliers : 4.36 % Allowed : 16.86 % Favored : 78.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.85 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.84 (0.34), residues: 468 helix: -4.92 (0.21), residues: 24 sheet: 0.44 (0.26), residues: 288 loop : -1.68 (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 B 87 PHE 0.009 0.002 PHE D 29 TYR 0.009 0.001 TYR B 96 ARG 0.003 0.001 ARG A 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: 15 poor density : 51 time to evaluate : 0.386 Fit side-chains REVERT: A 52 SER cc_start: 0.6864 (m) cc_final: 0.6499 (m) REVERT: A 53 ARG cc_start: 0.7784 (ttm110) cc_final: 0.7511 (mtt-85) REVERT: B 52 SER cc_start: 0.6775 (OUTLIER) cc_final: 0.6308 (m) REVERT: C 52 SER cc_start: 0.6818 (OUTLIER) cc_final: 0.6360 (m) REVERT: C 53 ARG cc_start: 0.7866 (mtt90) cc_final: 0.7465 (mtm-85) REVERT: D 52 SER cc_start: 0.6773 (m) cc_final: 0.6403 (m) REVERT: D 53 ARG cc_start: 0.7720 (ttm110) cc_final: 0.7439 (mtt-85) outliers start: 15 outliers final: 10 residues processed: 63 average time/residue: 1.2028 time to fit residues: 78.2018 Evaluate side-chains 57 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 45 time to evaluate : 0.380 ------------------------------------------------------------------------------- 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 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 4 optimal weight: 3.9990 chunk 41 optimal weight: 5.9990 chunk 15 optimal weight: 4.9990 chunk 22 optimal weight: 20.0000 chunk 12 optimal weight: 4.9990 chunk 16 optimal weight: 10.0000 chunk 26 optimal weight: 10.0000 chunk 24 optimal weight: 3.9990 chunk 23 optimal weight: 5.9990 chunk 25 optimal weight: 3.9990 chunk 27 optimal weight: 0.4980 overall best weight: 3.4988 ------------------------------------------------------------------------------- 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 = 0.3964 r_free = 0.3964 target = 0.171105 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.139399 restraints weight = 3068.630| |-----------------------------------------------------------------------------| r_work (start): 0.3586 rms_B_bonded: 1.41 r_work: 0.3445 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.3319 rms_B_bonded: 3.34 restraints_weight: 0.2500 r_work (final): 0.3319 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 moved from start: 0.3104 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= 0.264 Angle : 0.808 7.455 4976 Z= 0.437 Chirality : 0.047 0.162 556 Planarity : 0.005 0.037 624 Dihedral : 8.142 54.774 512 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.85 % Allowed : 4.91 % Favored : 94.23 % Rotamer: Outliers : 5.81 % Allowed : 15.70 % Favored : 78.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.85 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.92 (0.34), residues: 468 helix: -4.91 (0.20), residues: 24 sheet: 0.41 (0.26), residues: 288 loop : -1.80 (0.41), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.003 TRP A 79 HIS 0.001 0.001 HIS B 87 PHE 0.010 0.002 PHE D 29 TYR 0.010 0.002 TYR B 96 ARG 0.002 0.000 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 67 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 47 time to evaluate : 0.378 Fit side-chains REVERT: A 52 SER cc_start: 0.6801 (m) cc_final: 0.6393 (m) REVERT: A 53 ARG cc_start: 0.7798 (ttm110) cc_final: 0.7491 (mtt-85) REVERT: B 52 SER cc_start: 0.6808 (OUTLIER) cc_final: 0.6311 (m) REVERT: C 52 SER cc_start: 0.6852 (OUTLIER) cc_final: 0.6365 (m) REVERT: C 53 ARG cc_start: 0.7856 (mtt90) cc_final: 0.7532 (mtt-85) REVERT: D 52 SER cc_start: 0.6830 (m) cc_final: 0.6436 (m) REVERT: D 53 ARG cc_start: 0.7775 (ttm110) cc_final: 0.7463 (mtt-85) outliers start: 20 outliers final: 12 residues processed: 62 average time/residue: 1.1670 time to fit residues: 74.7045 Evaluate side-chains 59 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 45 time to evaluate : 0.349 ------------------------------------------------------------------------------- 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: 9.9990 chunk 5 optimal weight: 5.9990 chunk 8 optimal weight: 5.9990 chunk 4 optimal weight: 2.9990 chunk 40 optimal weight: 8.9990 chunk 24 optimal weight: 9.9990 chunk 15 optimal weight: 5.9990 chunk 43 optimal weight: 6.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- 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 = 0.3935 r_free = 0.3935 target = 0.168317 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.135811 restraints weight = 3077.866| |-----------------------------------------------------------------------------| r_work (start): 0.3546 rms_B_bonded: 1.47 r_work: 0.3403 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.3277 rms_B_bonded: 3.36 restraints_weight: 0.2500 r_work (final): 0.3277 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8412 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 : 0.006 0.041 3636 Z= 0.367 Angle : 0.879 7.765 4976 Z= 0.474 Chirality : 0.050 0.148 556 Planarity : 0.005 0.042 624 Dihedral : 8.187 48.727 512 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 1.71 % Allowed : 4.70 % Favored : 93.59 % Rotamer: Outliers : 4.65 % Allowed : 16.57 % Favored : 78.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.85 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.01 (0.33), residues: 468 helix: -4.69 (0.27), residues: 24 sheet: 0.40 (0.26), residues: 288 loop : -2.03 (0.40), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.004 TRP D 79 HIS 0.002 0.001 HIS B 87 PHE 0.012 0.003 PHE D 29 TYR 0.010 0.002 TYR A 22 ARG 0.003 0.001 ARG C 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 61 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 45 time to evaluate : 0.389 Fit side-chains REVERT: A 52 SER cc_start: 0.6770 (m) cc_final: 0.6340 (m) REVERT: B 52 SER cc_start: 0.6770 (OUTLIER) cc_final: 0.6233 (m) REVERT: C 52 SER cc_start: 0.6794 (OUTLIER) cc_final: 0.6281 (m) REVERT: C 53 ARG cc_start: 0.7821 (mtt90) cc_final: 0.7511 (mtt-85) REVERT: D 52 SER cc_start: 0.6833 (m) cc_final: 0.6411 (m) outliers start: 16 outliers final: 10 residues processed: 56 average time/residue: 1.2904 time to fit residues: 74.4306 Evaluate side-chains 56 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 44 time to evaluate : 0.345 ------------------------------------------------------------------------------- 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 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: 4.9990 chunk 25 optimal weight: 5.9990 chunk 7 optimal weight: 7.9990 chunk 41 optimal weight: 0.9990 chunk 32 optimal weight: 3.9990 chunk 5 optimal weight: 10.0000 chunk 19 optimal weight: 5.9990 chunk 31 optimal weight: 2.9990 chunk 26 optimal weight: 0.9990 chunk 11 optimal weight: 9.9990 chunk 10 optimal weight: 0.0570 overall best weight: 1.8106 ------------------------------------------------------------------------------- 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 = 0.3983 r_free = 0.3983 target = 0.172020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.140317 restraints weight = 2989.021| |-----------------------------------------------------------------------------| r_work (start): 0.3601 rms_B_bonded: 1.43 r_work: 0.3462 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.3338 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.3338 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8367 moved from start: 0.3292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3636 Z= 0.187 Angle : 0.731 6.472 4976 Z= 0.393 Chirality : 0.045 0.137 556 Planarity : 0.003 0.027 624 Dihedral : 6.874 34.679 512 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.85 % Allowed : 5.13 % Favored : 94.02 % Rotamer: Outliers : 4.36 % Allowed : 15.70 % Favored : 79.94 % 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: -0.72 (0.35), residues: 468 helix: -4.81 (0.24), residues: 24 sheet: 0.54 (0.26), residues: 288 loop : -1.66 (0.43), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP D 108 HIS 0.001 0.000 HIS D 87 PHE 0.008 0.002 PHE A 29 TYR 0.011 0.001 TYR D 96 ARG 0.001 0.000 ARG A 59 *********************** 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 71 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 56 time to evaluate : 0.353 Fit side-chains REVERT: A 52 SER cc_start: 0.6842 (m) cc_final: 0.6399 (m) REVERT: A 88 SER cc_start: 0.8884 (p) cc_final: 0.8641 (m) REVERT: B 52 SER cc_start: 0.6768 (OUTLIER) cc_final: 0.6253 (m) REVERT: B 88 SER cc_start: 0.8872 (p) cc_final: 0.8632 (m) REVERT: C 52 SER cc_start: 0.6817 (OUTLIER) cc_final: 0.6308 (m) REVERT: C 53 ARG cc_start: 0.7729 (mtt90) cc_final: 0.7451 (mtt-85) REVERT: D 52 SER cc_start: 0.6829 (m) cc_final: 0.6398 (m) REVERT: D 88 SER cc_start: 0.8889 (p) cc_final: 0.8642 (m) outliers start: 15 outliers final: 5 residues processed: 62 average time/residue: 1.2129 time to fit residues: 77.5611 Evaluate side-chains 59 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 52 time to evaluate : 0.374 ------------------------------------------------------------------------------- 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 1 optimal weight: 20.0000 chunk 34 optimal weight: 10.0000 chunk 19 optimal weight: 10.0000 chunk 35 optimal weight: 8.9990 chunk 40 optimal weight: 30.0000 chunk 13 optimal weight: 9.9990 chunk 16 optimal weight: 9.9990 chunk 12 optimal weight: 9.9990 chunk 22 optimal weight: 20.0000 chunk 6 optimal weight: 10.0000 chunk 17 optimal weight: 7.9990 overall best weight: 9.3990 ------------------------------------------------------------------------------- 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 = 0.3922 r_free = 0.3922 target = 0.167196 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.135139 restraints weight = 3032.366| |-----------------------------------------------------------------------------| r_work (start): 0.3532 rms_B_bonded: 1.43 r_work: 0.3379 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3253 rms_B_bonded: 3.36 restraints_weight: 0.2500 r_work (final): 0.3253 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8440 moved from start: 0.3563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.059 3636 Z= 0.551 Angle : 0.988 8.044 4976 Z= 0.532 Chirality : 0.057 0.168 556 Planarity : 0.007 0.054 624 Dihedral : 7.653 23.605 512 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.85 % Allowed : 6.84 % Favored : 92.31 % Rotamer: Outliers : 4.94 % Allowed : 16.86 % 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: -1.25 (0.32), residues: 468 helix: -4.57 (0.31), residues: 24 sheet: 0.33 (0.25), residues: 288 loop : -2.45 (0.38), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.005 TRP D 120 HIS 0.003 0.002 HIS C 87 PHE 0.014 0.004 PHE D 29 TYR 0.015 0.004 TYR C 22 ARG 0.003 0.001 ARG A 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 59 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 42 time to evaluate : 0.362 Fit side-chains REVERT: B 52 SER cc_start: 0.6615 (OUTLIER) cc_final: 0.5999 (m) REVERT: C 52 SER cc_start: 0.6713 (OUTLIER) cc_final: 0.6116 (m) REVERT: C 53 ARG cc_start: 0.7826 (mtt90) cc_final: 0.7490 (mtt-85) outliers start: 17 outliers final: 12 residues processed: 53 average time/residue: 1.3729 time to fit residues: 74.8364 Evaluate side-chains 56 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 42 time to evaluate : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 69 SER Chi-restraints excluded: chain B residue 25 LEU 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 25 LEU Chi-restraints excluded: chain C residue 39 LEU Chi-restraints excluded: chain C residue 52 SER Chi-restraints excluded: chain D residue 25 LEU 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: 0.6980 chunk 5 optimal weight: 9.9990 chunk 15 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 32 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 40 optimal weight: 5.9990 chunk 12 optimal weight: 9.9990 chunk 6 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- 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 = 0.3971 r_free = 0.3971 target = 0.171179 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.139737 restraints weight = 2986.898| |-----------------------------------------------------------------------------| r_work (start): 0.3597 rms_B_bonded: 1.42 r_work: 0.3458 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.3332 rms_B_bonded: 3.34 restraints_weight: 0.2500 r_work (final): 0.3332 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8375 moved from start: 0.3414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3636 Z= 0.193 Angle : 0.730 6.357 4976 Z= 0.392 Chirality : 0.045 0.139 556 Planarity : 0.004 0.028 624 Dihedral : 6.662 24.716 512 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.85 % Allowed : 4.49 % Favored : 94.66 % 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 : 0.00 % 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: -0.97 (0.35), residues: 468 helix: -4.88 (0.21), residues: 24 sheet: 0.30 (0.27), residues: 296 loop : -1.76 (0.45), residues: 148 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 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 A 22 ARG 0.003 0.001 ARG D 84 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 50 time to evaluate : 0.311 Fit side-chains REVERT: A 39 LEU cc_start: 0.8384 (OUTLIER) cc_final: 0.7979 (mp) REVERT: A 88 SER cc_start: 0.8889 (p) cc_final: 0.8622 (m) REVERT: B 52 SER cc_start: 0.6749 (OUTLIER) cc_final: 0.6218 (m) REVERT: B 88 SER cc_start: 0.8866 (p) cc_final: 0.8624 (m) REVERT: C 39 LEU cc_start: 0.8373 (OUTLIER) cc_final: 0.7980 (mp) REVERT: C 52 SER cc_start: 0.6763 (OUTLIER) cc_final: 0.6244 (m) REVERT: C 53 ARG cc_start: 0.7746 (mtt90) cc_final: 0.7365 (mtm-85) REVERT: C 88 SER cc_start: 0.8879 (p) cc_final: 0.8627 (m) REVERT: D 39 LEU cc_start: 0.8367 (OUTLIER) cc_final: 0.7978 (mp) REVERT: D 88 SER cc_start: 0.8893 (p) cc_final: 0.8634 (m) outliers start: 12 outliers final: 2 residues processed: 54 average time/residue: 1.3181 time to fit residues: 73.2748 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 : 0.377 ------------------------------------------------------------------------------- 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: 6.9990 chunk 43 optimal weight: 5.9990 chunk 16 optimal weight: 4.9990 chunk 36 optimal weight: 7.9990 chunk 24 optimal weight: 10.0000 chunk 1 optimal weight: 20.0000 chunk 10 optimal weight: 1.9990 chunk 3 optimal weight: 7.9990 chunk 31 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 12 optimal weight: 20.0000 overall best weight: 5.5990 ------------------------------------------------------------------------------- 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 = 0.3935 r_free = 0.3935 target = 0.168166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.135770 restraints weight = 3008.099| |-----------------------------------------------------------------------------| r_work (start): 0.3547 rms_B_bonded: 1.46 r_work: 0.3399 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3271 rms_B_bonded: 3.39 restraints_weight: 0.2500 r_work (final): 0.3271 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8425 moved from start: 0.3509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.041 3636 Z= 0.368 Angle : 0.880 7.658 4976 Z= 0.469 Chirality : 0.051 0.155 556 Planarity : 0.005 0.044 624 Dihedral : 7.276 23.859 512 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.85 % Allowed : 5.98 % Favored : 93.16 % Rotamer: Outliers : 2.33 % Allowed : 19.48 % 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: -1.03 (0.33), residues: 468 helix: -4.52 (0.35), residues: 24 sheet: 0.42 (0.25), residues: 288 loop : -2.16 (0.40), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.003 TRP D 120 HIS 0.002 0.001 HIS C 87 PHE 0.012 0.003 PHE D 29 TYR 0.015 0.003 TYR A 22 ARG 0.002 0.000 ARG D 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 49 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 41 time to evaluate : 0.373 Fit side-chains REVERT: B 52 SER cc_start: 0.6694 (OUTLIER) cc_final: 0.6101 (m) REVERT: C 52 SER cc_start: 0.6742 (OUTLIER) cc_final: 0.6172 (m) REVERT: C 53 ARG cc_start: 0.7819 (mtt90) cc_final: 0.7512 (mtt-85) outliers start: 8 outliers final: 5 residues processed: 47 average time/residue: 1.5346 time to fit residues: 74.0568 Evaluate side-chains 48 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 41 time to evaluate : 0.383 ------------------------------------------------------------------------------- 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 6 optimal weight: 7.9990 chunk 26 optimal weight: 7.9990 chunk 10 optimal weight: 0.4980 chunk 22 optimal weight: 10.0000 chunk 33 optimal weight: 20.0000 chunk 32 optimal weight: 5.9990 chunk 14 optimal weight: 0.0570 chunk 23 optimal weight: 3.9990 chunk 17 optimal weight: 0.9980 chunk 38 optimal weight: 9.9990 chunk 9 optimal weight: 7.9990 overall best weight: 2.3102 ------------------------------------------------------------------------------- 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 = 0.3961 r_free = 0.3961 target = 0.170232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.138864 restraints weight = 3020.158| |-----------------------------------------------------------------------------| r_work (start): 0.3587 rms_B_bonded: 1.43 r_work: 0.3446 rms_B_bonded: 2.06 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: 0.8385 moved from start: 0.3440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3636 Z= 0.213 Angle : 0.758 6.652 4976 Z= 0.405 Chirality : 0.045 0.137 556 Planarity : 0.003 0.031 624 Dihedral : 6.750 26.336 512 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.85 % Allowed : 4.27 % Favored : 94.87 % Rotamer: Outliers : 2.03 % Allowed : 19.48 % Favored : 78.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.87 (0.34), residues: 468 helix: -4.75 (0.25), residues: 24 sheet: 0.52 (0.26), residues: 288 loop : -1.96 (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 0.009 0.002 PHE D 29 TYR 0.012 0.001 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: 3180.99 seconds wall clock time: 55 minutes 12.90 seconds (3312.90 seconds total)