Starting phenix.real_space_refine on Wed Sep 25 06:13:13 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bzw_30261/09_2024/7bzw_30261.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bzw_30261/09_2024/7bzw_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bzw_30261/09_2024/7bzw_30261.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bzw_30261/09_2024/7bzw_30261.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bzw_30261/09_2024/7bzw_30261.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bzw_30261/09_2024/7bzw_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-5461/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: 6.02, per 1000 atoms: 0.62 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: 2.67 Conformation dependent library (CDL) restraints added in 1.2 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: 1.27 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: 2.46 Time building geometry restraints manager: 3.11 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: 0.00 Found NCS groups: ncs_group { reference = chain '1' selection = chain '10' selection = chain '11' selection = chain '12' selection = chain '2' selection = chain '3' selection = chain '4' selection = chain '5' selection = chain '6' selection = chain '7' selection = chain '8' selection = chain '9' } Set up NCS constraints Number of NCS constrained groups: 1 pdb_interpretation.ncs_group { reference = chain '1' selection = chain '10' selection = chain '11' selection = chain '12' selection = chain '2' selection = chain '3' selection = chain '4' selection = chain '5' selection = chain '6' selection = chain '7' selection = chain '8' selection = chain '9' } 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: 0.770 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: 0.360 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 25.310 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.050 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:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.820 ------------------------------------------------------------------------------- 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 33 residues out of total 94 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 33 time to evaluate : 0.109 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 217 VAL cc_start: 0.8057 (t) cc_final: 0.7734 (p) outliers start: 0 outliers final: 0 residues processed: 33 average time/residue: 0.2129 time to fit residues: 7.4359 Evaluate side-chains 18 residues out of total 94 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 18 time to evaluate : 0.112 ------------------------------------------------------------------------------- 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: 10.0000 chunk 90 optimal weight: 9.9990 chunk 50 optimal weight: 9.9990 chunk 31 optimal weight: 8.9990 chunk 61 optimal weight: 9.9990 chunk 48 optimal weight: 0.0030 chunk 94 optimal weight: 3.9990 chunk 36 optimal weight: 0.9990 chunk 57 optimal weight: 0.3980 chunk 70 optimal weight: 10.0000 chunk 108 optimal weight: 0.6980 overall best weight: 1.2194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 9 167 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6932 moved from start: 0.4538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 9888 Z= 0.225 Angle : 0.786 4.266 13260 Z= 0.419 Chirality : 0.054 0.164 1476 Planarity : 0.006 0.050 1704 Dihedral : 7.140 27.957 1260 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 19.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 19.19 % Favored : 80.81 % 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: -4.36 (0.22), residues: 1188 helix: None (None), residues: 0 sheet: -2.02 (0.22), residues: 456 loop : -3.69 (0.21), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP 3 176 HIS 0.000 0.000 HIS 1 136 PHE 0.011 0.003 PHE 2 142 TYR 0.008 0.004 TYR 5 184 ARG 0.002 0.001 ARG 1 187 *********************** 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 24 residues out of total 94 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 24 time to evaluate : 0.095 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 9 210 ILE cc_start: 0.7920 (mp) cc_final: 0.6932 (mp) REVERT: 9 217 VAL cc_start: 0.7844 (t) cc_final: 0.7156 (p) outliers start: 0 outliers final: 0 residues processed: 24 average time/residue: 0.1951 time to fit residues: 5.0034 Evaluate side-chains 14 residues out of total 94 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 14 time to evaluate : 0.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 60 optimal weight: 10.0000 chunk 33 optimal weight: 0.5980 chunk 90 optimal weight: 10.0000 chunk 74 optimal weight: 0.1980 chunk 30 optimal weight: 10.0000 chunk 109 optimal weight: 3.9990 chunk 117 optimal weight: 0.0070 chunk 97 optimal weight: 0.5980 chunk 108 optimal weight: 8.9990 chunk 37 optimal weight: 1.9990 chunk 87 optimal weight: 0.0770 overall best weight: 0.2956 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6763 moved from start: 0.5175 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= 0.199 Angle : 0.732 5.377 13260 Z= 0.386 Chirality : 0.054 0.199 1476 Planarity : 0.005 0.046 1704 Dihedral : 6.389 25.526 1260 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 14.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.16 % Favored : 83.84 % Rotamer: Outliers : 0.00 % Allowed : 6.38 % Favored : 93.62 % 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: -3.69 (0.23), residues: 1188 helix: None (None), residues: 0 sheet: -1.32 (0.23), residues: 456 loop : -3.41 (0.22), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP 2 176 HIS 0.000 0.000 HIS 7 136 PHE 0.011 0.003 PHE 1 142 TYR 0.007 0.002 TYR 6 184 ARG 0.001 0.000 ARG 1 187 *********************** 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 23 residues out of total 94 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 23 time to evaluate : 0.107 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 6 203 LEU cc_start: 0.8089 (tp) cc_final: 0.7263 (pt) REVERT: 6 217 VAL cc_start: 0.7880 (t) cc_final: 0.7425 (t) outliers start: 0 outliers final: 0 residues processed: 23 average time/residue: 0.1873 time to fit residues: 4.6164 Evaluate side-chains 15 residues out of total 94 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 15 time to evaluate : 0.105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 107 optimal weight: 0.0570 chunk 82 optimal weight: 7.9990 chunk 56 optimal weight: 0.0370 chunk 12 optimal weight: 7.9990 chunk 52 optimal weight: 7.9990 chunk 73 optimal weight: 0.0070 chunk 109 optimal weight: 2.9990 chunk 115 optimal weight: 10.0000 chunk 57 optimal weight: 0.9990 chunk 103 optimal weight: 0.0060 chunk 31 optimal weight: 0.0980 overall best weight: 0.0410 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6690 moved from start: 0.6017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9888 Z= 0.223 Angle : 0.747 5.819 13260 Z= 0.391 Chirality : 0.055 0.215 1476 Planarity : 0.005 0.043 1704 Dihedral : 6.306 19.892 1260 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 15.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 17.17 % Favored : 82.83 % 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: -3.13 (0.22), residues: 1188 helix: None (None), residues: 0 sheet: -0.56 (0.22), residues: 456 loop : -3.33 (0.21), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP 5 176 HIS 0.002 0.001 HIS 7 136 PHE 0.012 0.003 PHE 6 209 TYR 0.006 0.002 TYR 6 184 ARG 0.002 0.000 ARG 7 187 *********************** REFINEMENT MACRO_CYCLE 4 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 22 residues out of total 94 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 22 time to evaluate : 0.102 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 11 210 ILE cc_start: 0.7776 (mp) cc_final: 0.6857 (mp) outliers start: 0 outliers final: 0 residues processed: 22 average time/residue: 0.1481 time to fit residues: 3.5744 Evaluate side-chains 15 residues out of total 94 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 15 time to evaluate : 0.105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 96 optimal weight: 0.8980 chunk 65 optimal weight: 8.9990 chunk 1 optimal weight: 5.9990 chunk 86 optimal weight: 0.8980 chunk 47 optimal weight: 0.0970 chunk 98 optimal weight: 9.9990 chunk 80 optimal weight: 9.9990 chunk 0 optimal weight: 9.9990 chunk 59 optimal weight: 0.3980 chunk 104 optimal weight: 10.0000 chunk 29 optimal weight: 0.0170 overall best weight: 0.4616 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6700 moved from start: 0.6655 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= 0.196 Angle : 0.737 6.224 13260 Z= 0.388 Chirality : 0.053 0.151 1476 Planarity : 0.005 0.043 1704 Dihedral : 6.156 18.542 1260 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 15.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.14 % Favored : 85.86 % 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: -3.13 (0.23), residues: 1188 helix: -5.57 (0.07), residues: 72 sheet: -0.74 (0.22), residues: 456 loop : -2.75 (0.24), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.003 TRP10 129 HIS 0.000 0.000 HIS 8 136 PHE 0.012 0.004 PHE12 209 TYR 0.016 0.004 TYR 2 184 ARG 0.001 0.000 ARG10 141 *********************** REFINEMENT MACRO_CYCLE 5 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 20 residues out of total 94 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 20 time to evaluate : 0.111 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 20 average time/residue: 0.1149 time to fit residues: 2.6134 Evaluate side-chains 15 residues out of total 94 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 15 time to evaluate : 0.109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 39 optimal weight: 0.7980 chunk 104 optimal weight: 9.9990 chunk 22 optimal weight: 8.9990 chunk 68 optimal weight: 0.8980 chunk 28 optimal weight: 0.0570 chunk 116 optimal weight: 0.5980 chunk 96 optimal weight: 0.4980 chunk 53 optimal weight: 10.0000 chunk 9 optimal weight: 2.9990 chunk 38 optimal weight: 0.0040 chunk 60 optimal weight: 8.9990 overall best weight: 0.3910 ------------------------------------------------------------------------------- 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 ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6657 moved from start: 0.7131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9888 Z= 0.209 Angle : 0.732 4.904 13260 Z= 0.386 Chirality : 0.051 0.186 1476 Planarity : 0.005 0.040 1704 Dihedral : 6.172 18.290 1260 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 15.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.15 % Favored : 84.85 % 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: -3.11 (0.23), residues: 1188 helix: None (None), residues: 0 sheet: -0.71 (0.22), residues: 456 loop : -3.18 (0.21), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP 6 176 HIS 0.009 0.006 HIS 4 136 PHE 0.011 0.003 PHE 6 209 TYR 0.003 0.002 TYR 7 184 ARG 0.001 0.000 ARG 7 187 *********************** 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 20 residues out of total 94 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 20 time to evaluate : 0.112 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 20 average time/residue: 0.1240 time to fit residues: 2.7992 Evaluate side-chains 14 residues out of total 94 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 14 time to evaluate : 0.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 111 optimal weight: 1.9990 chunk 13 optimal weight: 0.0970 chunk 66 optimal weight: 0.2980 chunk 84 optimal weight: 7.9990 chunk 65 optimal weight: 6.9990 chunk 97 optimal weight: 0.7980 chunk 64 optimal weight: 9.9990 chunk 115 optimal weight: 5.9990 chunk 72 optimal weight: 7.9990 chunk 70 optimal weight: 10.0000 chunk 53 optimal weight: 0.0000 overall best weight: 0.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6699 moved from start: 0.7790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 9888 Z= 0.214 Angle : 0.761 6.098 13260 Z= 0.400 Chirality : 0.053 0.229 1476 Planarity : 0.005 0.040 1704 Dihedral : 6.314 26.644 1260 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 13.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.14 % Favored : 85.86 % Rotamer: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % 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: -0.32 (0.25), residues: 456 loop : -3.17 (0.21), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP 7 176 HIS 0.001 0.001 HIS 9 136 PHE 0.016 0.003 PHE 6 209 TYR 0.003 0.001 TYR 9 184 ARG 0.004 0.001 ARG 1 219 *********************** 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 18 residues out of total 94 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 18 time to evaluate : 0.096 Fit side-chains revert: symmetry clash REVERT: 11 147 LEU cc_start: 0.5888 (tp) cc_final: 0.4526 (tp) outliers start: 0 outliers final: 0 residues processed: 18 average time/residue: 0.0737 time to fit residues: 1.6111 Evaluate side-chains 15 residues out of total 94 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 15 time to evaluate : 0.105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 71 optimal weight: 3.9990 chunk 46 optimal weight: 0.4980 chunk 69 optimal weight: 8.9990 chunk 34 optimal weight: 0.9990 chunk 22 optimal weight: 8.9990 chunk 73 optimal weight: 0.0270 chunk 78 optimal weight: 0.0570 chunk 57 optimal weight: 0.6980 chunk 10 optimal weight: 10.0000 chunk 90 optimal weight: 9.9990 chunk 105 optimal weight: 6.9990 overall best weight: 0.4558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6673 moved from start: 0.8157 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= 0.214 Angle : 0.784 7.850 13260 Z= 0.400 Chirality : 0.055 0.178 1476 Planarity : 0.005 0.042 1704 Dihedral : 6.521 21.938 1260 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 13.98 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: -2.78 (0.23), residues: 1188 helix: None (None), residues: 0 sheet: -0.36 (0.22), residues: 492 loop : -3.17 (0.21), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP10 129 HIS 0.000 0.000 HIS 2 136 PHE 0.016 0.003 PHE11 209 TYR 0.006 0.002 TYR 2 184 ARG 0.002 0.000 ARG11 179 *********************** 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 17 residues out of total 94 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 17 time to evaluate : 0.121 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 17 average time/residue: 0.0772 time to fit residues: 1.6177 Evaluate side-chains 14 residues out of total 94 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 14 time to evaluate : 0.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 110 optimal weight: 9.9990 chunk 101 optimal weight: 10.0000 chunk 107 optimal weight: 0.7980 chunk 64 optimal weight: 10.0000 chunk 46 optimal weight: 3.9990 chunk 84 optimal weight: 6.9990 chunk 33 optimal weight: 0.0470 chunk 97 optimal weight: 0.7980 chunk 70 optimal weight: 8.9990 chunk 113 optimal weight: 0.0970 chunk 69 optimal weight: 6.9990 overall best weight: 1.1478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6727 moved from start: 0.8454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 9888 Z= 0.223 Angle : 0.771 7.603 13260 Z= 0.397 Chirality : 0.054 0.175 1476 Planarity : 0.005 0.042 1704 Dihedral : 6.413 19.198 1260 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 19.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.13 % Favored : 86.87 % 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: -2.71 (0.22), residues: 1188 helix: None (None), residues: 0 sheet: -0.49 (0.23), residues: 456 loop : -2.86 (0.20), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP 9 129 HIS 0.000 0.000 HIS 2 136 PHE 0.018 0.004 PHE 6 209 TYR 0.003 0.001 TYR 9 184 ARG 0.002 0.001 ARG 7 179 *********************** 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 16 residues out of total 94 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 16 time to evaluate : 0.112 Fit side-chains revert: symmetry clash REVERT: 11 131 ILE cc_start: 0.7849 (mp) cc_final: 0.6470 (mp) REVERT: 11 203 LEU cc_start: 0.7561 (tp) cc_final: 0.6883 (pt) outliers start: 0 outliers final: 0 residues processed: 16 average time/residue: 0.0748 time to fit residues: 1.4835 Evaluate side-chains 13 residues out of total 94 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 13 time to evaluate : 0.109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 54 optimal weight: 7.9990 chunk 79 optimal weight: 0.0970 chunk 119 optimal weight: 3.9990 chunk 110 optimal weight: 9.9990 chunk 95 optimal weight: 6.9990 chunk 9 optimal weight: 0.9990 chunk 73 optimal weight: 0.0980 chunk 58 optimal weight: 0.0030 chunk 75 optimal weight: 7.9990 chunk 101 optimal weight: 6.9990 chunk 29 optimal weight: 4.9990 overall best weight: 1.0392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6720 moved from start: 0.8648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 9888 Z= 0.249 Angle : 0.893 7.872 13260 Z= 0.447 Chirality : 0.061 0.230 1476 Planarity : 0.006 0.043 1704 Dihedral : 6.463 19.259 1260 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 19.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.14 % Favored : 85.86 % Rotamer: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % 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: -2.84 (0.23), residues: 1188 helix: None (None), residues: 0 sheet: -0.89 (0.21), residues: 516 loop : -2.82 (0.22), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP 9 129 HIS 0.001 0.001 HIS12 136 PHE 0.021 0.004 PHE10 209 TYR 0.001 0.001 TYR 9 184 ARG 0.002 0.001 ARG 8 179 ********************** 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 16 residues out of total 94 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 16 time to evaluate : 0.100 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 16 average time/residue: 0.1056 time to fit residues: 1.9666 Evaluate side-chains 14 residues out of total 94 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 14 time to evaluate : 0.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 87 optimal weight: 0.8980 chunk 14 optimal weight: 8.9990 chunk 26 optimal weight: 0.5980 chunk 95 optimal weight: 5.9990 chunk 39 optimal weight: 0.7980 chunk 97 optimal weight: 0.0870 chunk 12 optimal weight: 0.0770 chunk 17 optimal weight: 0.0970 chunk 83 optimal weight: 4.9990 chunk 5 optimal weight: 6.9990 chunk 68 optimal weight: 9.9990 overall best weight: 0.3314 ------------------------------------------------------------------------------- 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 = 0.3238 r_free = 0.3238 target = 0.043282 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.033391 restraints weight = 9259.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.034098 restraints weight = 7111.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.034602 restraints weight = 5918.437| |-----------------------------------------------------------------------------| r_work (final): 0.2995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8645 moved from start: 0.8837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9888 Z= 0.222 Angle : 0.865 7.734 13260 Z= 0.438 Chirality : 0.056 0.216 1476 Planarity : 0.005 0.042 1704 Dihedral : 6.321 20.071 1260 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 16.98 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: -2.90 (0.22), residues: 1188 helix: None (None), residues: 0 sheet: -0.84 (0.21), residues: 516 loop : -2.96 (0.21), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP 3 176 HIS 0.001 0.001 HIS 2 136 PHE 0.024 0.006 PHE 6 142 TYR 0.002 0.001 TYR 4 184 ARG 0.002 0.001 ARG 9 179 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1921.57 seconds wall clock time: 35 minutes 15.92 seconds (2115.92 seconds total)