Starting phenix.real_space_refine on Fri Feb 14 02:59:23 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7bzw_30261/02_2025/7bzw_30261.cif Found real_map, /net/cci-nas-00/data/ceres_data/7bzw_30261/02_2025/7bzw_30261.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7bzw_30261/02_2025/7bzw_30261.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7bzw_30261/02_2025/7bzw_30261.map" model { file = "/net/cci-nas-00/data/ceres_data/7bzw_30261/02_2025/7bzw_30261.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7bzw_30261/02_2025/7bzw_30261.cif" } resolution = 4.6 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= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 36 5.16 5 C 6120 2.51 5 N 1656 2.21 5 O 1944 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 84 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 9756 Number of models: 1 Model: "" Number of chains: 12 Chain: "1" Number of atoms: 813 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 813 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 4, 'TRANS': 96} Chain: "2" Number of atoms: 813 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 813 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 4, 'TRANS': 96} Chain: "3" Number of atoms: 813 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 813 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 4, 'TRANS': 96} Chain: "4" Number of atoms: 813 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 813 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 4, 'TRANS': 96} Chain: "5" Number of atoms: 813 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 813 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 4, 'TRANS': 96} Chain: "6" Number of atoms: 813 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 813 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 4, 'TRANS': 96} Chain: "7" Number of atoms: 813 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 813 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 4, 'TRANS': 96} Chain: "8" Number of atoms: 813 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 813 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 4, 'TRANS': 96} Chain: "9" Number of atoms: 813 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 813 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 4, 'TRANS': 96} Chain: "10" Number of atoms: 813 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 813 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 4, 'TRANS': 96} Chain: "11" Number of atoms: 813 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 813 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 4, 'TRANS': 96} Chain: "12" Number of atoms: 813 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 813 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 4, 'TRANS': 96} Time building chain proxies: 5.50, per 1000 atoms: 0.56 Number of scatterers: 9756 At special positions: 0 Unit cell: (113.42, 114.48, 104.94, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 36 16.00 O 1944 8.00 N 1656 7.00 C 6120 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: 2.32 Conformation dependent library (CDL) restraints added in 1.1 seconds 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2304 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 24 sheets defined 0.0% alpha, 29.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.10 Creating SS restraints... Processing sheet with id=AA1, first strand: chain '1' and resid 130 through 133 Processing sheet with id=AA2, first strand: chain '1' and resid 152 through 155 Processing sheet with id=AA3, first strand: chain '2' and resid 130 through 133 Processing sheet with id=AA4, first strand: chain '2' and resid 152 through 155 Processing sheet with id=AA5, first strand: chain '3' and resid 130 through 133 Processing sheet with id=AA6, first strand: chain '3' and resid 152 through 155 Processing sheet with id=AA7, first strand: chain '4' and resid 130 through 133 Processing sheet with id=AA8, first strand: chain '4' and resid 152 through 155 Processing sheet with id=AA9, first strand: chain '5' and resid 130 through 133 Processing sheet with id=AB1, first strand: chain '5' and resid 152 through 155 Processing sheet with id=AB2, first strand: chain '6' and resid 130 through 133 Processing sheet with id=AB3, first strand: chain '6' and resid 152 through 155 Processing sheet with id=AB4, first strand: chain '7' and resid 130 through 133 Processing sheet with id=AB5, first strand: chain '7' and resid 152 through 155 Processing sheet with id=AB6, first strand: chain '8' and resid 130 through 133 Processing sheet with id=AB7, first strand: chain '8' and resid 152 through 155 Processing sheet with id=AB8, first strand: chain '9' and resid 130 through 133 Processing sheet with id=AB9, first strand: chain '9' and resid 152 through 155 Processing sheet with id=AC1, first strand: chain '10' and resid 130 through 133 Processing sheet with id=AC2, first strand: chain '10' and resid 152 through 155 Processing sheet with id=AC3, first strand: chain '11' and resid 130 through 133 Processing sheet with id=AC4, first strand: chain '11' and resid 152 through 155 Processing sheet with id=AC5, first strand: chain '12' and resid 130 through 133 Processing sheet with id=AC6, first strand: chain '12' and resid 152 through 155 288 hydrogen bonds defined for protein. 720 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: 2.28 Time building geometry restraints manager: 2.69 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3252 1.34 - 1.46: 1639 1.46 - 1.58: 4937 1.58 - 1.69: 0 1.69 - 1.81: 60 Bond restraints: 9888 Sorted by residual: bond pdb=" CA GLY 4 165 " pdb=" C GLY 4 165 " ideal model delta sigma weight residual 1.516 1.509 0.007 1.01e-02 9.80e+03 4.95e-01 bond pdb=" N LYS11 216 " pdb=" CA LYS11 216 " ideal model delta sigma weight residual 1.457 1.466 -0.009 1.29e-02 6.01e+03 4.86e-01 bond pdb=" N GLY 6 165 " pdb=" CA GLY 6 165 " ideal model delta sigma weight residual 1.451 1.443 0.008 1.16e-02 7.43e+03 4.84e-01 bond pdb=" N GLY12 165 " pdb=" CA GLY12 165 " ideal model delta sigma weight residual 1.451 1.443 0.008 1.16e-02 7.43e+03 4.82e-01 bond pdb=" N GLY 7 165 " pdb=" CA GLY 7 165 " ideal model delta sigma weight residual 1.451 1.443 0.008 1.16e-02 7.43e+03 4.74e-01 ... (remaining 9883 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.92: 10934 0.92 - 1.85: 1741 1.85 - 2.77: 388 2.77 - 3.69: 113 3.69 - 4.61: 84 Bond angle restraints: 13260 Sorted by residual: angle pdb=" C ILE 6 131 " pdb=" N LYS 6 132 " pdb=" CA LYS 6 132 " ideal model delta sigma weight residual 121.63 117.02 4.61 1.92e+00 2.71e-01 5.78e+00 angle pdb=" C ILE 2 131 " pdb=" N LYS 2 132 " pdb=" CA LYS 2 132 " ideal model delta sigma weight residual 121.63 117.03 4.60 1.92e+00 2.71e-01 5.73e+00 angle pdb=" C ILE 8 131 " pdb=" N LYS 8 132 " pdb=" CA LYS 8 132 " ideal model delta sigma weight residual 121.63 117.04 4.59 1.92e+00 2.71e-01 5.71e+00 angle pdb=" C ILE10 131 " pdb=" N LYS10 132 " pdb=" CA LYS10 132 " ideal model delta sigma weight residual 121.63 117.04 4.59 1.92e+00 2.71e-01 5.71e+00 angle pdb=" C ILE 7 131 " pdb=" N LYS 7 132 " pdb=" CA LYS 7 132 " ideal model delta sigma weight residual 121.63 117.05 4.58 1.92e+00 2.71e-01 5.69e+00 ... (remaining 13255 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.42: 4716 11.42 - 22.84: 935 22.84 - 34.26: 469 34.26 - 45.67: 72 45.67 - 57.09: 60 Dihedral angle restraints: 6252 sinusoidal: 2736 harmonic: 3516 Sorted by residual: dihedral pdb=" CA GLU 9 195 " pdb=" C GLU 9 195 " pdb=" N LYS 9 196 " pdb=" CA LYS 9 196 " ideal model delta harmonic sigma weight residual -180.00 -160.18 -19.82 0 5.00e+00 4.00e-02 1.57e+01 dihedral pdb=" CA GLU 4 195 " pdb=" C GLU 4 195 " pdb=" N LYS 4 196 " pdb=" CA LYS 4 196 " ideal model delta harmonic sigma weight residual -180.00 -160.19 -19.81 0 5.00e+00 4.00e-02 1.57e+01 dihedral pdb=" CA GLU 5 195 " pdb=" C GLU 5 195 " pdb=" N LYS 5 196 " pdb=" CA LYS 5 196 " ideal model delta harmonic sigma weight residual 180.00 -160.20 -19.80 0 5.00e+00 4.00e-02 1.57e+01 ... (remaining 6249 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 650 0.028 - 0.056: 426 0.056 - 0.085: 229 0.085 - 0.113: 89 0.113 - 0.141: 82 Chirality restraints: 1476 Sorted by residual: chirality pdb=" CA ILE 3 138 " pdb=" N ILE 3 138 " pdb=" C ILE 3 138 " pdb=" CB ILE 3 138 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.96e-01 chirality pdb=" CA ILE 8 138 " pdb=" N ILE 8 138 " pdb=" C ILE 8 138 " pdb=" CB ILE 8 138 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.94e-01 chirality pdb=" CA ILE 6 138 " pdb=" N ILE 6 138 " pdb=" C ILE 6 138 " pdb=" CB ILE 6 138 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.92e-01 ... (remaining 1473 not shown) Planarity restraints: 1704 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU 4 190 " 0.035 5.00e-02 4.00e+02 5.31e-02 4.52e+00 pdb=" N PRO 4 191 " -0.092 5.00e-02 4.00e+02 pdb=" CA PRO 4 191 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO 4 191 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU 2 190 " -0.035 5.00e-02 4.00e+02 5.31e-02 4.50e+00 pdb=" N PRO 2 191 " 0.092 5.00e-02 4.00e+02 pdb=" CA PRO 2 191 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO 2 191 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU 5 190 " -0.035 5.00e-02 4.00e+02 5.31e-02 4.50e+00 pdb=" N PRO 5 191 " 0.092 5.00e-02 4.00e+02 pdb=" CA PRO 5 191 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO 5 191 " -0.029 5.00e-02 4.00e+02 ... (remaining 1701 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 740 2.72 - 3.27: 10669 3.27 - 3.81: 15449 3.81 - 4.36: 18051 4.36 - 4.90: 28123 Nonbonded interactions: 73032 Sorted by model distance: nonbonded pdb=" OE1 GLN 9 167 " pdb=" OH TYR 9 184 " model vdw 2.176 3.040 nonbonded pdb=" OE1 GLN 5 167 " pdb=" OH TYR 5 184 " model vdw 2.176 3.040 nonbonded pdb=" OE1 GLN 3 167 " pdb=" OH TYR 3 184 " model vdw 2.176 3.040 nonbonded pdb=" OE1 GLN11 167 " pdb=" OH TYR11 184 " model vdw 2.176 3.040 nonbonded pdb=" OE1 GLN 4 167 " pdb=" OH TYR 4 184 " model vdw 2.176 3.040 ... (remaining 73027 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: 0.08 Found NCS groups: ncs_group { reference = chain '11' selection = chain '10' selection = chain '12' selection = chain '1' selection = chain '3' selection = chain '2' selection = chain '5' selection = chain '4' selection = chain '7' selection = chain '6' selection = chain '9' selection = chain '8' } Set up NCS constraints Number of NCS constrained groups: 1 pdb_interpretation.ncs_group { reference = chain '11' selection = chain '10' selection = chain '12' selection = chain '1' selection = chain '3' selection = chain '2' selection = chain '5' selection = chain '4' selection = chain '7' selection = chain '6' selection = chain '9' selection = chain '8' } Set refine NCS operators NCS operators will be refined. 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 group one per residue 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: 0.640 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.400 Check model and map are aligned: 0.080 Set scattering table: 0.090 Process input model: 22.720 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6947 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 : 0.003 0.020 9888 Z= 0.227 Angle : 0.823 4.614 13260 Z= 0.458 Chirality : 0.054 0.141 1476 Planarity : 0.006 0.053 1704 Dihedral : 15.818 57.093 3948 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 28.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 19.36 % Favored : 80.64 % Rotamer: Outliers : 0.00 % Allowed : 8.51 % Favored : 91.49 % 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: -5.59 (0.20), residues: 1188 helix: -5.58 (0.06), residues: 72 sheet: -3.01 (0.21), residues: 420 loop : -4.13 (0.20), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP10 129 HIS 0.001 0.000 HIS 4 136 PHE 0.005 0.001 PHE 5 142 TYR 0.009 0.003 TYR11 184 ARG 0.003 0.000 ARG 6 187 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 30 residues out of total 94 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 30 time to evaluate : 0.116 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 11 217 VAL cc_start: 0.8028 (t) cc_final: 0.7742 (p) outliers start: 0 outliers final: 0 residues processed: 30 average time/residue: 0.1873 time to fit residues: 6.0064 Evaluate side-chains 18 residues out of total 94 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 18 time to evaluate : 0.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 101 optimal weight: 8.9990 chunk 90 optimal weight: 9.9990 chunk 50 optimal weight: 9.9990 chunk 31 optimal weight: 1.9990 chunk 61 optimal weight: 9.9990 chunk 48 optimal weight: 0.7980 chunk 94 optimal weight: 20.0000 chunk 36 optimal weight: 0.0870 chunk 57 optimal weight: 6.9990 chunk 70 optimal weight: 10.0000 chunk 108 optimal weight: 0.0270 overall best weight: 1.9820 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3 167 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.038221 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2779 r_free = 0.2779 target = 0.029084 restraints weight = 9972.219| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2797 r_free = 0.2797 target = 0.029685 restraints weight = 7495.332| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2810 r_free = 0.2810 target = 0.030123 restraints weight = 6160.583| |-----------------------------------------------------------------------------| r_work (final): 0.2789 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8898 moved from start: 0.3841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 9888 Z= 0.250 Angle : 0.786 3.924 13260 Z= 0.420 Chirality : 0.056 0.163 1476 Planarity : 0.006 0.052 1704 Dihedral : 7.386 27.520 1260 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 22.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 19.19 % Favored : 80.81 % Rotamer: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.54 (0.22), residues: 1188 helix: None (None), residues: 0 sheet: -2.10 (0.23), residues: 432 loop : -3.81 (0.20), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP 4 176 HIS 0.000 0.000 HIS 1 136 PHE 0.008 0.002 PHE 2 142 TYR 0.010 0.003 TYR 7 184 ARG 0.002 0.001 ARG 6 179 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2178 Ramachandran restraints generated. 1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2178 Ramachandran restraints generated. 1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 20 residues out of total 94 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 20 time to evaluate : 0.104 Fit side-chains revert: symmetry clash REVERT: 3 196 LYS cc_start: 0.7986 (tttt) cc_final: 0.7677 (mptt) REVERT: 3 210 ILE cc_start: 0.9495 (mp) cc_final: 0.9040 (mp) REVERT: 3 223 ASP cc_start: 0.5919 (t0) cc_final: 0.5646 (t0) outliers start: 0 outliers final: 0 residues processed: 20 average time/residue: 0.1903 time to fit residues: 4.1524 Evaluate side-chains 16 residues out of total 94 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 16 time to evaluate : 0.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 15 optimal weight: 10.0000 chunk 47 optimal weight: 0.5980 chunk 117 optimal weight: 0.0020 chunk 61 optimal weight: 9.9990 chunk 9 optimal weight: 0.0670 chunk 91 optimal weight: 6.9990 chunk 93 optimal weight: 0.3980 chunk 92 optimal weight: 9.9990 chunk 68 optimal weight: 0.0470 chunk 83 optimal weight: 0.3980 chunk 25 optimal weight: 10.0000 overall best weight: 0.1824 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.042429 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.032456 restraints weight = 9454.047| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.033050 restraints weight = 7143.776| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.033545 restraints weight = 5973.974| |-----------------------------------------------------------------------------| r_work (final): 0.2940 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8776 moved from start: 0.4903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 9888 Z= 0.186 Angle : 0.731 5.465 13260 Z= 0.386 Chirality : 0.056 0.200 1476 Planarity : 0.005 0.045 1704 Dihedral : 6.189 21.723 1260 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 12.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.15 % Favored : 84.85 % Rotamer: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % 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: -3.81 (0.22), residues: 1188 helix: None (None), residues: 0 sheet: -1.31 (0.23), residues: 432 loop : -3.51 (0.20), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP 2 176 HIS 0.000 0.000 HIS 5 136 PHE 0.013 0.003 PHE 5 209 TYR 0.006 0.002 TYR 2 184 ARG 0.003 0.001 ARG 6 141 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1980 Ramachandran restraints generated. 990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1980 Ramachandran restraints generated. 990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 24 residues out of total 94 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 24 time to evaluate : 0.111 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 8 131 ILE cc_start: 0.9492 (mm) cc_final: 0.9182 (mm) REVERT: 8 196 LYS cc_start: 0.8109 (tttt) cc_final: 0.7694 (mptt) REVERT: 8 217 VAL cc_start: 0.8811 (p) cc_final: 0.8413 (p) outliers start: 0 outliers final: 0 residues processed: 24 average time/residue: 0.1995 time to fit residues: 5.1295 Evaluate side-chains 20 residues out of total 94 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 20 time to evaluate : 0.093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 108 optimal weight: 0.0170 chunk 101 optimal weight: 4.9990 chunk 66 optimal weight: 0.8980 chunk 23 optimal weight: 2.9990 chunk 5 optimal weight: 7.9990 chunk 16 optimal weight: 0.0970 chunk 53 optimal weight: 2.9990 chunk 80 optimal weight: 9.9990 chunk 26 optimal weight: 0.0170 chunk 82 optimal weight: 1.9990 chunk 103 optimal weight: 0.5980 overall best weight: 0.3254 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.042414 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2883 r_free = 0.2883 target = 0.032508 restraints weight = 9181.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2904 r_free = 0.2904 target = 0.033162 restraints weight = 6817.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 21)----------------| | r_work = 0.2920 r_free = 0.2920 target = 0.033642 restraints weight = 5588.174| |-----------------------------------------------------------------------------| r_work (final): 0.2899 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8764 moved from start: 0.5465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9888 Z= 0.205 Angle : 0.726 5.638 13260 Z= 0.384 Chirality : 0.055 0.208 1476 Planarity : 0.005 0.044 1704 Dihedral : 6.294 21.502 1260 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 13.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.14 % Favored : 85.86 % Rotamer: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % 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: -3.43 (0.22), residues: 1188 helix: None (None), residues: 0 sheet: -0.89 (0.22), residues: 432 loop : -3.37 (0.20), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP 2 176 HIS 0.001 0.001 HIS 7 136 PHE 0.008 0.002 PHE 6 209 TYR 0.006 0.002 TYR 6 184 ARG 0.003 0.001 ARG 1 187 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1980 Ramachandran restraints generated. 990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1980 Ramachandran restraints generated. 990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 22 residues out of total 94 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 22 time to evaluate : 0.096 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 8 196 LYS cc_start: 0.9170 (ttmm) cc_final: 0.8944 (mptt) REVERT: 8 210 ILE cc_start: 0.9676 (mp) cc_final: 0.8878 (mp) outliers start: 0 outliers final: 0 residues processed: 22 average time/residue: 0.1880 time to fit residues: 4.4519 Evaluate side-chains 17 residues out of total 94 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 17 time to evaluate : 0.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 111 optimal weight: 0.0570 chunk 12 optimal weight: 9.9990 chunk 29 optimal weight: 0.4980 chunk 5 optimal weight: 6.9990 chunk 103 optimal weight: 8.9990 chunk 82 optimal weight: 8.9990 chunk 70 optimal weight: 7.9990 chunk 55 optimal weight: 7.9990 chunk 31 optimal weight: 0.0870 chunk 84 optimal weight: 7.9990 chunk 95 optimal weight: 6.9990 overall best weight: 2.9280 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.037878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2813 r_free = 0.2813 target = 0.029375 restraints weight = 10319.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2831 r_free = 0.2831 target = 0.029976 restraints weight = 7579.756| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2843 r_free = 0.2843 target = 0.030390 restraints weight = 6134.022| |-----------------------------------------------------------------------------| r_work (final): 0.2815 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8889 moved from start: 0.5508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 9888 Z= 0.263 Angle : 0.734 7.569 13260 Z= 0.399 Chirality : 0.054 0.159 1476 Planarity : 0.006 0.047 1704 Dihedral : 6.831 22.483 1260 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 26.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 17.17 % Favored : 82.83 % Rotamer: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % 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: -3.54 (0.22), residues: 1188 helix: None (None), residues: 0 sheet: -1.29 (0.20), residues: 492 loop : -3.33 (0.23), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP 1 129 HIS 0.000 0.000 HIS 7 136 PHE 0.007 0.002 PHE 3 142 TYR 0.005 0.003 TYR 9 184 ARG 0.003 0.001 ARG 1 179 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1980 Ramachandran restraints generated. 990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1980 Ramachandran restraints generated. 990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 21 residues out of total 94 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 21 time to evaluate : 0.099 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 21 average time/residue: 0.1488 time to fit residues: 3.4353 Evaluate side-chains 19 residues out of total 94 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 19 time to evaluate : 0.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 106 optimal weight: 0.9980 chunk 96 optimal weight: 0.1980 chunk 111 optimal weight: 7.9990 chunk 70 optimal weight: 10.0000 chunk 39 optimal weight: 3.9990 chunk 57 optimal weight: 0.0870 chunk 59 optimal weight: 0.9980 chunk 29 optimal weight: 1.9990 chunk 104 optimal weight: 4.9990 chunk 7 optimal weight: 0.5980 chunk 117 optimal weight: 0.0570 overall best weight: 0.3876 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 11 136 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.040867 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2909 r_free = 0.2909 target = 0.031876 restraints weight = 9516.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2931 r_free = 0.2931 target = 0.032541 restraints weight = 7080.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.033014 restraints weight = 5807.987| |-----------------------------------------------------------------------------| r_work (final): 0.2927 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8775 moved from start: 0.6197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 9888 Z= 0.204 Angle : 0.743 6.506 13260 Z= 0.392 Chirality : 0.052 0.146 1476 Planarity : 0.005 0.049 1704 Dihedral : 6.408 20.285 1260 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 17.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.14 % Favored : 85.86 % Rotamer: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -3.21 (0.22), residues: 1188 helix: None (None), residues: 0 sheet: -0.56 (0.23), residues: 432 loop : -3.33 (0.20), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.003 TRP10 129 HIS 0.008 0.005 HIS 4 136 PHE 0.011 0.003 PHE 2 142 TYR 0.005 0.002 TYR11 184 ARG 0.002 0.001 ARG 9 141 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1782 Ramachandran restraints generated. 891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1782 Ramachandran restraints generated. 891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 23 residues out of total 94 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 23 time to evaluate : 0.120 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 11 147 LEU cc_start: 0.8304 (tp) cc_final: 0.7868 (tp) REVERT: 11 210 ILE cc_start: 0.9549 (mp) cc_final: 0.9230 (mp) REVERT: 11 222 ILE cc_start: 0.6911 (pt) cc_final: 0.6589 (mp) REVERT: 11 223 ASP cc_start: 0.7145 (t0) cc_final: 0.6648 (t0) outliers start: 0 outliers final: 0 residues processed: 23 average time/residue: 0.1494 time to fit residues: 3.7982 Evaluate side-chains 19 residues out of total 94 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 19 time to evaluate : 0.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 10 optimal weight: 9.9990 chunk 112 optimal weight: 8.9990 chunk 90 optimal weight: 7.9990 chunk 16 optimal weight: 6.9990 chunk 28 optimal weight: 3.9990 chunk 78 optimal weight: 3.9990 chunk 116 optimal weight: 0.0670 chunk 25 optimal weight: 6.9990 chunk 101 optimal weight: 6.9990 chunk 52 optimal weight: 7.9990 chunk 102 optimal weight: 10.0000 overall best weight: 4.4126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 11 136 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.036965 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2793 r_free = 0.2793 target = 0.028408 restraints weight = 10366.851| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2807 r_free = 0.2807 target = 0.028845 restraints weight = 8477.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2816 r_free = 0.2816 target = 0.029156 restraints weight = 7380.062| |-----------------------------------------------------------------------------| r_work (final): 0.2787 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8996 moved from start: 0.6815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 9888 Z= 0.332 Angle : 0.722 4.237 13260 Z= 0.395 Chirality : 0.053 0.149 1476 Planarity : 0.007 0.051 1704 Dihedral : 6.976 23.289 1260 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 33.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 17.17 % Favored : 82.83 % Rotamer: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % 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: -4.09 (0.23), residues: 1188 helix: None (None), residues: 0 sheet: -2.15 (0.21), residues: 516 loop : -3.28 (0.24), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP 9 176 HIS 0.002 0.001 HIS 4 136 PHE 0.013 0.003 PHE 2 142 TYR 0.005 0.003 TYR 3 184 ARG 0.004 0.001 ARG 2 179 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1782 Ramachandran restraints generated. 891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1782 Ramachandran restraints generated. 891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 19 residues out of total 94 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 19 time to evaluate : 0.096 Fit side-chains revert: symmetry clash REVERT: 11 223 ASP cc_start: 0.7470 (t0) cc_final: 0.6945 (t0) outliers start: 0 outliers final: 0 residues processed: 19 average time/residue: 0.0897 time to fit residues: 2.0041 Evaluate side-chains 11 residues out of total 94 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 11 time to evaluate : 0.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 8 optimal weight: 0.0060 chunk 11 optimal weight: 4.9990 chunk 89 optimal weight: 3.9990 chunk 64 optimal weight: 8.9990 chunk 77 optimal weight: 0.1980 chunk 35 optimal weight: 8.9990 chunk 52 optimal weight: 6.9990 chunk 40 optimal weight: 7.9990 chunk 78 optimal weight: 0.0060 chunk 54 optimal weight: 10.0000 chunk 13 optimal weight: 0.7980 overall best weight: 1.0014 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.038875 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2837 r_free = 0.2837 target = 0.029799 restraints weight = 9756.426| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2858 r_free = 0.2858 target = 0.030439 restraints weight = 7229.444| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2872 r_free = 0.2872 target = 0.030885 restraints weight = 5901.577| |-----------------------------------------------------------------------------| r_work (final): 0.2849 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8870 moved from start: 0.6855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 9888 Z= 0.190 Angle : 0.686 4.458 13260 Z= 0.363 Chirality : 0.052 0.153 1476 Planarity : 0.005 0.050 1704 Dihedral : 6.150 20.308 1260 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 16.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 17.17 % Favored : 82.83 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.84 (0.22), residues: 1188 helix: None (None), residues: 0 sheet: -1.94 (0.20), residues: 456 loop : -3.11 (0.22), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP 5 176 HIS 0.001 0.000 HIS 4 136 PHE 0.011 0.002 PHE 4 209 TYR 0.006 0.003 TYR 4 184 ARG 0.002 0.000 ARG 6 187 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1782 Ramachandran restraints generated. 891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1782 Ramachandran restraints generated. 891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 18 residues out of total 94 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 18 time to evaluate : 0.111 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 18 average time/residue: 0.0679 time to fit residues: 1.5192 Evaluate side-chains 16 residues out of total 94 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 16 time to evaluate : 0.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 34 optimal weight: 5.9990 chunk 66 optimal weight: 20.0000 chunk 82 optimal weight: 6.9990 chunk 49 optimal weight: 0.7980 chunk 38 optimal weight: 0.0000 chunk 84 optimal weight: 4.9990 chunk 117 optimal weight: 0.0040 chunk 104 optimal weight: 0.4980 chunk 59 optimal weight: 1.9990 chunk 15 optimal weight: 8.9990 chunk 79 optimal weight: 0.7980 overall best weight: 0.4196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.039796 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2894 r_free = 0.2894 target = 0.030745 restraints weight = 9622.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 21)----------------| | r_work = 0.2916 r_free = 0.2916 target = 0.031470 restraints weight = 6937.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2930 r_free = 0.2930 target = 0.031958 restraints weight = 5586.809| |-----------------------------------------------------------------------------| r_work (final): 0.2909 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8819 moved from start: 0.7257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 9888 Z= 0.195 Angle : 0.737 5.075 13260 Z= 0.394 Chirality : 0.052 0.149 1476 Planarity : 0.005 0.047 1704 Dihedral : 5.951 17.081 1260 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 15.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 17.17 % Favored : 82.83 % Rotamer: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -3.24 (0.23), residues: 1188 helix: None (None), residues: 0 sheet: -1.46 (0.21), residues: 456 loop : -2.74 (0.23), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP 2 176 HIS 0.000 0.000 HIS 4 136 PHE 0.014 0.003 PHE11 209 TYR 0.007 0.002 TYR 2 184 ARG 0.002 0.000 ARG 6 141 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1782 Ramachandran restraints generated. 891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1782 Ramachandran restraints generated. 891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 21 residues out of total 94 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 21 time to evaluate : 0.102 Fit side-chains revert: symmetry clash REVERT: 11 147 LEU cc_start: 0.7789 (tp) cc_final: 0.7569 (tp) REVERT: 11 210 ILE cc_start: 0.9550 (mp) cc_final: 0.9288 (mp) outliers start: 0 outliers final: 0 residues processed: 21 average time/residue: 0.0933 time to fit residues: 2.2848 Evaluate side-chains 16 residues out of total 94 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 16 time to evaluate : 0.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 3 optimal weight: 0.7980 chunk 19 optimal weight: 0.7980 chunk 84 optimal weight: 0.0980 chunk 37 optimal weight: 3.9990 chunk 59 optimal weight: 0.8980 chunk 74 optimal weight: 0.7980 chunk 48 optimal weight: 0.4980 chunk 70 optimal weight: 9.9990 chunk 38 optimal weight: 1.9990 chunk 76 optimal weight: 0.5980 chunk 20 optimal weight: 9.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.041098 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2921 r_free = 0.2921 target = 0.031545 restraints weight = 9498.240| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.032155 restraints weight = 7222.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.032602 restraints weight = 6039.255| |-----------------------------------------------------------------------------| r_work (final): 0.2920 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8780 moved from start: 0.7483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 9888 Z= 0.193 Angle : 0.741 4.839 13260 Z= 0.382 Chirality : 0.053 0.147 1476 Planarity : 0.006 0.047 1704 Dihedral : 5.744 15.639 1260 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 14.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.14 % Favored : 85.86 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.88 (0.23), residues: 1188 helix: None (None), residues: 0 sheet: -1.38 (0.21), residues: 456 loop : -2.35 (0.24), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP 9 176 HIS 0.000 0.000 HIS 4 136 PHE 0.015 0.003 PHE 7 209 TYR 0.002 0.001 TYR10 184 ARG 0.001 0.000 ARG 6 187 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1782 Ramachandran restraints generated. 891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1782 Ramachandran restraints generated. 891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 18 residues out of total 94 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 18 time to evaluate : 0.101 Fit side-chains revert: symmetry clash REVERT: 11 210 ILE cc_start: 0.9512 (mp) cc_final: 0.9274 (mp) REVERT: 11 223 ASP cc_start: 0.7622 (t0) cc_final: 0.7308 (t0) outliers start: 0 outliers final: 0 residues processed: 18 average time/residue: 0.0684 time to fit residues: 1.5262 Evaluate side-chains 14 residues out of total 94 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 14 time to evaluate : 0.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 23 optimal weight: 8.9990 chunk 8 optimal weight: 0.9980 chunk 96 optimal weight: 0.0970 chunk 103 optimal weight: 8.9990 chunk 21 optimal weight: 8.9990 chunk 97 optimal weight: 0.7980 chunk 27 optimal weight: 2.9990 chunk 95 optimal weight: 6.9990 chunk 82 optimal weight: 5.9990 chunk 55 optimal weight: 10.0000 chunk 47 optimal weight: 2.9990 overall best weight: 1.5782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.041245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2885 r_free = 0.2885 target = 0.031412 restraints weight = 9872.062| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2898 r_free = 0.2898 target = 0.031875 restraints weight = 8230.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2907 r_free = 0.2907 target = 0.032197 restraints weight = 7237.717| |-----------------------------------------------------------------------------| r_work (final): 0.2883 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8829 moved from start: 0.7839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 9888 Z= 0.218 Angle : 0.751 4.446 13260 Z= 0.394 Chirality : 0.056 0.165 1476 Planarity : 0.006 0.048 1704 Dihedral : 6.155 15.706 1260 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 16.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.14 % Favored : 85.86 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.85 (0.23), residues: 1188 helix: None (None), residues: 0 sheet: -1.69 (0.21), residues: 456 loop : -2.07 (0.24), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP 5 176 HIS 0.000 0.000 HIS 4 136 PHE 0.012 0.004 PHE10 142 TYR 0.002 0.001 TYR12 184 ARG 0.003 0.001 ARG 5 141 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2051.38 seconds wall clock time: 38 minutes 0.61 seconds (2280.61 seconds total)