Starting phenix.real_space_refine on Fri Aug 2 13:41:24 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xh6_38342/08_2024/8xh6_38342_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xh6_38342/08_2024/8xh6_38342.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.52 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xh6_38342/08_2024/8xh6_38342.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xh6_38342/08_2024/8xh6_38342.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xh6_38342/08_2024/8xh6_38342_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xh6_38342/08_2024/8xh6_38342_neut.cif" } resolution = 3.52 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= 0.001 sd= 0.083 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 14 5.16 5 C 1870 2.51 5 N 378 2.21 5 O 372 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 128": "OE1" <-> "OE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 2634 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 1317 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 1317 Classifications: {'peptide': 161} Link IDs: {'PTRANS': 1, 'TRANS': 159} Chain: "B" Number of atoms: 1317 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 1317 Classifications: {'peptide': 161} Link IDs: {'PTRANS': 1, 'TRANS': 159} Time building chain proxies: 2.29, per 1000 atoms: 0.87 Number of scatterers: 2634 At special positions: 0 Unit cell: (57.2, 71.76, 70.72, 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 14 16.00 O 372 8.00 N 378 7.00 C 1870 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.90 Conformation dependent library (CDL) restraints added in 452.6 milliseconds 636 Ramachandran restraints generated. 318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 600 Finding SS restraints... Secondary structure from input PDB file: 14 helices and 0 sheets defined 90.1% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.23 Creating SS restraints... Processing helix chain 'A' and resid 24 through 45 removed outlier: 4.261A pdb=" N LEU A 37 " --> pdb=" O LEU A 33 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LEU A 40 " --> pdb=" O LEU A 36 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N TYR A 41 " --> pdb=" O LEU A 37 " (cutoff:3.500A) Processing helix chain 'A' and resid 50 through 72 removed outlier: 4.057A pdb=" N VAL A 54 " --> pdb=" O GLY A 50 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N LEU A 55 " --> pdb=" O ALA A 51 " (cutoff:3.500A) Processing helix chain 'A' and resid 73 through 77 removed outlier: 3.821A pdb=" N LEU A 76 " --> pdb=" O ARG A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 80 through 99 removed outlier: 4.399A pdb=" N ASN A 99 " --> pdb=" O ILE A 95 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 132 removed outlier: 4.115A pdb=" N LEU A 107 " --> pdb=" O GLN A 103 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LEU A 111 " --> pdb=" O LEU A 107 " (cutoff:3.500A) Processing helix chain 'A' and resid 136 through 160 Processing helix chain 'A' and resid 162 through 183 removed outlier: 3.534A pdb=" N THR A 166 " --> pdb=" O GLN A 162 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU A 168 " --> pdb=" O TRP A 164 " (cutoff:3.500A) Processing helix chain 'B' and resid 25 through 44 removed outlier: 3.734A pdb=" N MET B 44 " --> pdb=" O LEU B 40 " (cutoff:3.500A) Processing helix chain 'B' and resid 52 through 72 Processing helix chain 'B' and resid 73 through 77 removed outlier: 3.874A pdb=" N LEU B 76 " --> pdb=" O ARG B 73 " (cutoff:3.500A) Processing helix chain 'B' and resid 80 through 100 removed outlier: 4.401A pdb=" N ILE B 95 " --> pdb=" O THR B 91 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ALA B 96 " --> pdb=" O LEU B 92 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N LEU B 100 " --> pdb=" O ALA B 96 " (cutoff:3.500A) Processing helix chain 'B' and resid 103 through 133 removed outlier: 4.065A pdb=" N LEU B 107 " --> pdb=" O GLN B 103 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LEU B 118 " --> pdb=" O PHE B 114 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N GLY B 121 " --> pdb=" O LEU B 117 " (cutoff:3.500A) Processing helix chain 'B' and resid 136 through 160 removed outlier: 3.744A pdb=" N PHE B 143 " --> pdb=" O GLN B 139 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N ILE B 144 " --> pdb=" O LEU B 140 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N TYR B 159 " --> pdb=" O ILE B 155 " (cutoff:3.500A) Processing helix chain 'B' and resid 164 through 183 removed outlier: 4.109A pdb=" N LEU B 181 " --> pdb=" O PHE B 177 " (cutoff:3.500A) 213 hydrogen bonds defined for protein. 633 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.64 Time building geometry restraints manager: 1.01 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: 703 1.34 - 1.46: 689 1.46 - 1.58: 1292 1.58 - 1.69: 0 1.69 - 1.81: 24 Bond restraints: 2708 Sorted by residual: bond pdb=" CA TRP A 131 " pdb=" C TRP A 131 " ideal model delta sigma weight residual 1.522 1.499 0.023 1.41e-02 5.03e+03 2.74e+00 bond pdb=" CG1 ILE B 95 " pdb=" CD1 ILE B 95 " ideal model delta sigma weight residual 1.513 1.473 0.040 3.90e-02 6.57e+02 1.03e+00 bond pdb=" CG LEU B 60 " pdb=" CD1 LEU B 60 " ideal model delta sigma weight residual 1.521 1.494 0.027 3.30e-02 9.18e+02 6.69e-01 bond pdb=" CG ARG A 74 " pdb=" CD ARG A 74 " ideal model delta sigma weight residual 1.520 1.543 -0.023 3.00e-02 1.11e+03 5.85e-01 bond pdb=" N MET A 184 " pdb=" CA MET A 184 " ideal model delta sigma weight residual 1.458 1.472 -0.014 1.90e-02 2.77e+03 5.06e-01 ... (remaining 2703 not shown) Histogram of bond angle deviations from ideal: 98.64 - 105.71: 17 105.71 - 112.78: 1560 112.78 - 119.86: 885 119.86 - 126.93: 1192 126.93 - 134.00: 54 Bond angle restraints: 3708 Sorted by residual: angle pdb=" C LEU A 130 " pdb=" N TRP A 131 " pdb=" CA TRP A 131 " ideal model delta sigma weight residual 120.60 125.40 -4.80 1.60e+00 3.91e-01 8.99e+00 angle pdb=" N ILE B 71 " pdb=" CA ILE B 71 " pdb=" C ILE B 71 " ideal model delta sigma weight residual 111.58 108.76 2.82 1.06e+00 8.90e-01 7.10e+00 angle pdb=" C TRP A 183 " pdb=" N MET A 184 " pdb=" CA MET A 184 " ideal model delta sigma weight residual 121.70 125.85 -4.15 1.80e+00 3.09e-01 5.31e+00 angle pdb=" CB MET A 61 " pdb=" CG MET A 61 " pdb=" SD MET A 61 " ideal model delta sigma weight residual 112.70 118.32 -5.62 3.00e+00 1.11e-01 3.51e+00 angle pdb=" C ILE A 109 " pdb=" CA ILE A 109 " pdb=" CB ILE A 109 " ideal model delta sigma weight residual 111.97 109.70 2.27 1.28e+00 6.10e-01 3.14e+00 ... (remaining 3703 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.00: 1320 16.00 - 32.01: 138 32.01 - 48.01: 31 48.01 - 64.02: 1 64.02 - 80.02: 4 Dihedral angle restraints: 1494 sinusoidal: 564 harmonic: 930 Sorted by residual: dihedral pdb=" CB MET B 89 " pdb=" CG MET B 89 " pdb=" SD MET B 89 " pdb=" CE MET B 89 " ideal model delta sinusoidal sigma weight residual 60.00 116.18 -56.18 3 1.50e+01 4.44e-03 9.39e+00 dihedral pdb=" CB GLU B 128 " pdb=" CG GLU B 128 " pdb=" CD GLU B 128 " pdb=" OE1 GLU B 128 " ideal model delta sinusoidal sigma weight residual 0.00 -80.02 80.02 1 3.00e+01 1.11e-03 8.82e+00 dihedral pdb=" CA LEU B 174 " pdb=" CB LEU B 174 " pdb=" CG LEU B 174 " pdb=" CD1 LEU B 174 " ideal model delta sinusoidal sigma weight residual 180.00 136.71 43.29 3 1.50e+01 4.44e-03 7.78e+00 ... (remaining 1491 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.021: 219 0.021 - 0.042: 137 0.042 - 0.063: 84 0.063 - 0.084: 27 0.084 - 0.106: 7 Chirality restraints: 474 Sorted by residual: chirality pdb=" CA CYS A 78 " pdb=" N CYS A 78 " pdb=" C CYS A 78 " pdb=" CB CYS A 78 " both_signs ideal model delta sigma weight residual False 2.51 2.40 0.11 2.00e-01 2.50e+01 2.78e-01 chirality pdb=" CA THR A 91 " pdb=" N THR A 91 " pdb=" C THR A 91 " pdb=" CB THR A 91 " both_signs ideal model delta sigma weight residual False 2.53 2.43 0.09 2.00e-01 2.50e+01 2.20e-01 chirality pdb=" CG LEU A 60 " pdb=" CB LEU A 60 " pdb=" CD1 LEU A 60 " pdb=" CD2 LEU A 60 " both_signs ideal model delta sigma weight residual False -2.59 -2.68 0.09 2.00e-01 2.50e+01 2.03e-01 ... (remaining 471 not shown) Planarity restraints: 402 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 74 " -0.102 9.50e-02 1.11e+02 4.62e-02 1.74e+00 pdb=" NE ARG A 74 " 0.010 2.00e-02 2.50e+03 pdb=" CZ ARG A 74 " -0.010 2.00e-02 2.50e+03 pdb=" NH1 ARG A 74 " 0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG A 74 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C CYS B 78 " 0.015 5.00e-02 4.00e+02 2.32e-02 8.59e-01 pdb=" N PRO B 79 " -0.040 5.00e-02 4.00e+02 pdb=" CA PRO B 79 " 0.011 5.00e-02 4.00e+02 pdb=" CD PRO B 79 " 0.013 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C CYS A 78 " -0.015 5.00e-02 4.00e+02 2.23e-02 7.95e-01 pdb=" N PRO A 79 " 0.039 5.00e-02 4.00e+02 pdb=" CA PRO A 79 " -0.011 5.00e-02 4.00e+02 pdb=" CD PRO A 79 " -0.013 5.00e-02 4.00e+02 ... (remaining 399 not shown) Histogram of nonbonded interaction distances: 2.40 - 2.90: 919 2.90 - 3.40: 2794 3.40 - 3.90: 4364 3.90 - 4.40: 4625 4.40 - 4.90: 7627 Nonbonded interactions: 20329 Sorted by model distance: nonbonded pdb=" OD1 ASN B 99 " pdb=" N LEU B 100 " model vdw 2.397 3.120 nonbonded pdb=" O ASN B 46 " pdb=" ND2 ASN B 163 " model vdw 2.406 3.120 nonbonded pdb=" O THR A 48 " pdb=" OG1 THR A 48 " model vdw 2.460 3.040 nonbonded pdb=" O PHE B 70 " pdb=" NE ARG B 74 " model vdw 2.590 3.120 nonbonded pdb=" OG SER B 45 " pdb=" N ASN B 46 " model vdw 2.616 3.120 ... (remaining 20324 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 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 0.890 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 12.350 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7236 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 0.040 2708 Z= 0.200 Angle : 0.586 6.169 3708 Z= 0.297 Chirality : 0.036 0.106 474 Planarity : 0.003 0.046 402 Dihedral : 14.079 80.022 894 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % 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: 1.24 (0.47), residues: 318 helix: 1.16 (0.31), residues: 284 sheet: None (None), residues: 0 loop : -1.56 (1.07), residues: 34 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 164 HIS 0.001 0.001 HIS A 101 PHE 0.011 0.001 PHE A 72 TYR 0.007 0.001 TYR A 159 ARG 0.012 0.001 ARG A 74 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 636 Ramachandran restraints generated. 318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 636 Ramachandran restraints generated. 318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 276 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 37 time to evaluate : 0.273 Fit side-chains REVERT: A 161 GLN cc_start: 0.6670 (mt0) cc_final: 0.6451 (mt0) outliers start: 0 outliers final: 0 residues processed: 37 average time/residue: 0.1228 time to fit residues: 5.7735 Evaluate side-chains 32 residues out of total 276 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 32 time to evaluate : 0.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 27 optimal weight: 3.9990 chunk 24 optimal weight: 0.6980 chunk 13 optimal weight: 0.6980 chunk 8 optimal weight: 0.0170 chunk 16 optimal weight: 1.9990 chunk 12 optimal weight: 0.6980 chunk 25 optimal weight: 0.6980 chunk 9 optimal weight: 0.5980 chunk 15 optimal weight: 1.9990 chunk 18 optimal weight: 0.7980 chunk 29 optimal weight: 1.9990 overall best weight: 0.5418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7274 moved from start: 0.1226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 2708 Z= 0.189 Angle : 0.523 5.791 3708 Z= 0.247 Chirality : 0.034 0.096 474 Planarity : 0.003 0.024 402 Dihedral : 3.757 10.372 336 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 0.72 % Allowed : 10.51 % Favored : 88.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.69 (0.46), residues: 318 helix: 1.42 (0.30), residues: 288 sheet: None (None), residues: 0 loop : -1.47 (1.15), residues: 30 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 131 HIS 0.001 0.001 HIS A 101 PHE 0.012 0.001 PHE A 38 TYR 0.005 0.001 TYR B 125 ARG 0.006 0.001 ARG A 74 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 636 Ramachandran restraints generated. 318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 636 Ramachandran restraints generated. 318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 276 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 40 time to evaluate : 0.288 Fit side-chains REVERT: A 161 GLN cc_start: 0.6809 (mt0) cc_final: 0.6497 (mt0) REVERT: B 184 MET cc_start: 0.5703 (tpp) cc_final: 0.5368 (mmm) outliers start: 2 outliers final: 1 residues processed: 41 average time/residue: 0.1071 time to fit residues: 5.6427 Evaluate side-chains 37 residues out of total 276 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 36 time to evaluate : 0.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 99 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 16 optimal weight: 2.9990 chunk 9 optimal weight: 0.7980 chunk 24 optimal weight: 1.9990 chunk 19 optimal weight: 0.9990 chunk 8 optimal weight: 1.9990 chunk 29 optimal weight: 0.9990 chunk 31 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 28 optimal weight: 0.7980 chunk 23 optimal weight: 0.9990 chunk 21 optimal weight: 0.0370 overall best weight: 0.7262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7337 moved from start: 0.1657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 2708 Z= 0.219 Angle : 0.520 5.786 3708 Z= 0.246 Chirality : 0.035 0.100 474 Planarity : 0.003 0.030 402 Dihedral : 3.715 11.428 336 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 2.54 % Allowed : 14.13 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.88 (0.46), residues: 318 helix: 1.55 (0.30), residues: 288 sheet: None (None), residues: 0 loop : -1.45 (1.14), residues: 30 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 131 HIS 0.001 0.000 HIS A 101 PHE 0.008 0.001 PHE A 177 TYR 0.006 0.001 TYR A 125 ARG 0.004 0.001 ARG A 74 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 636 Ramachandran restraints generated. 318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 636 Ramachandran restraints generated. 318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 276 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 38 time to evaluate : 0.273 Fit side-chains REVERT: A 161 GLN cc_start: 0.6824 (mt0) cc_final: 0.6571 (mt0) REVERT: B 147 PHE cc_start: 0.8567 (t80) cc_final: 0.8164 (t80) outliers start: 7 outliers final: 6 residues processed: 42 average time/residue: 0.1337 time to fit residues: 6.9718 Evaluate side-chains 43 residues out of total 276 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 37 time to evaluate : 0.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain B residue 99 ASN Chi-restraints excluded: chain B residue 100 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 15 optimal weight: 0.5980 chunk 3 optimal weight: 0.5980 chunk 13 optimal weight: 0.2980 chunk 19 optimal weight: 0.4980 chunk 29 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 27 optimal weight: 3.9990 chunk 8 optimal weight: 0.4980 chunk 25 optimal weight: 2.9990 chunk 17 optimal weight: 0.5980 chunk 0 optimal weight: 4.9990 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7313 moved from start: 0.1814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 2708 Z= 0.168 Angle : 0.475 5.935 3708 Z= 0.227 Chirality : 0.034 0.099 474 Planarity : 0.002 0.025 402 Dihedral : 3.645 11.105 336 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 2.54 % Allowed : 19.20 % Favored : 78.26 % 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: 2.24 (0.47), residues: 318 helix: 1.77 (0.30), residues: 288 sheet: None (None), residues: 0 loop : -1.20 (1.22), residues: 30 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 39 HIS 0.001 0.000 HIS A 101 PHE 0.008 0.001 PHE A 177 TYR 0.007 0.001 TYR A 125 ARG 0.003 0.000 ARG A 74 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 636 Ramachandran restraints generated. 318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 636 Ramachandran restraints generated. 318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 276 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 36 time to evaluate : 0.289 Fit side-chains REVERT: A 86 LEU cc_start: 0.7929 (OUTLIER) cc_final: 0.7690 (tt) REVERT: A 129 ILE cc_start: 0.7566 (OUTLIER) cc_final: 0.7317 (mm) REVERT: B 147 PHE cc_start: 0.8581 (t80) cc_final: 0.8163 (t80) REVERT: B 184 MET cc_start: 0.6290 (tpp) cc_final: 0.5430 (mmt) outliers start: 7 outliers final: 4 residues processed: 41 average time/residue: 0.1487 time to fit residues: 7.5688 Evaluate side-chains 41 residues out of total 276 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 35 time to evaluate : 0.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain B residue 99 ASN Chi-restraints excluded: chain B residue 100 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 23 optimal weight: 0.9980 chunk 12 optimal weight: 0.7980 chunk 26 optimal weight: 0.9980 chunk 21 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 chunk 15 optimal weight: 0.9980 chunk 27 optimal weight: 1.9990 chunk 7 optimal weight: 0.9990 chunk 10 optimal weight: 0.8980 chunk 6 optimal weight: 0.5980 chunk 18 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7384 moved from start: 0.2014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 2708 Z= 0.242 Angle : 0.532 6.019 3708 Z= 0.250 Chirality : 0.035 0.106 474 Planarity : 0.002 0.028 402 Dihedral : 3.733 11.930 336 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 4.71 % Allowed : 19.93 % Favored : 75.36 % 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: 2.20 (0.46), residues: 318 helix: 1.75 (0.30), residues: 288 sheet: None (None), residues: 0 loop : -1.16 (1.22), residues: 30 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 131 HIS 0.001 0.000 HIS A 101 PHE 0.008 0.001 PHE A 177 TYR 0.004 0.001 TYR A 125 ARG 0.002 0.000 ARG A 74 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 636 Ramachandran restraints generated. 318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 636 Ramachandran restraints generated. 318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 276 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 33 time to evaluate : 0.280 Fit side-chains REVERT: A 159 TYR cc_start: 0.6734 (m-10) cc_final: 0.6457 (m-80) REVERT: A 161 GLN cc_start: 0.6851 (mt0) cc_final: 0.6567 (mt0) REVERT: B 147 PHE cc_start: 0.8562 (t80) cc_final: 0.8145 (t80) REVERT: B 184 MET cc_start: 0.6086 (tpp) cc_final: 0.5410 (mmt) outliers start: 13 outliers final: 6 residues processed: 45 average time/residue: 0.1297 time to fit residues: 7.2286 Evaluate side-chains 38 residues out of total 276 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 32 time to evaluate : 0.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain B residue 100 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 7 optimal weight: 0.8980 chunk 30 optimal weight: 0.3980 chunk 25 optimal weight: 0.8980 chunk 14 optimal weight: 0.5980 chunk 2 optimal weight: 0.9980 chunk 10 optimal weight: 0.9980 chunk 16 optimal weight: 1.9990 chunk 29 optimal weight: 0.5980 chunk 3 optimal weight: 0.3980 chunk 17 optimal weight: 0.7980 chunk 22 optimal weight: 0.6980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7344 moved from start: 0.2132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 2708 Z= 0.175 Angle : 0.490 6.741 3708 Z= 0.231 Chirality : 0.034 0.100 474 Planarity : 0.002 0.025 402 Dihedral : 3.637 11.213 336 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 3.62 % Allowed : 21.01 % Favored : 75.36 % 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: 2.50 (0.46), residues: 318 helix: 1.94 (0.29), residues: 288 sheet: None (None), residues: 0 loop : -0.99 (1.22), residues: 30 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 131 HIS 0.001 0.000 HIS A 101 PHE 0.007 0.001 PHE A 177 TYR 0.005 0.001 TYR A 125 ARG 0.002 0.000 ARG A 132 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 636 Ramachandran restraints generated. 318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 636 Ramachandran restraints generated. 318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 276 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 36 time to evaluate : 0.281 Fit side-chains REVERT: A 159 TYR cc_start: 0.6780 (m-10) cc_final: 0.6512 (m-80) REVERT: A 161 GLN cc_start: 0.6782 (mt0) cc_final: 0.6503 (mt0) REVERT: A 172 LEU cc_start: 0.7739 (tt) cc_final: 0.7263 (mt) REVERT: B 147 PHE cc_start: 0.8591 (t80) cc_final: 0.8200 (t80) REVERT: B 184 MET cc_start: 0.5713 (tpp) cc_final: 0.5341 (mmm) outliers start: 10 outliers final: 6 residues processed: 46 average time/residue: 0.1492 time to fit residues: 8.3750 Evaluate side-chains 39 residues out of total 276 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 33 time to evaluate : 0.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain B residue 42 ILE Chi-restraints excluded: chain B residue 100 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 17 optimal weight: 0.9990 chunk 26 optimal weight: 4.9990 chunk 30 optimal weight: 1.9990 chunk 19 optimal weight: 0.5980 chunk 18 optimal weight: 1.9990 chunk 14 optimal weight: 0.6980 chunk 12 optimal weight: 0.6980 chunk 9 optimal weight: 0.9990 chunk 6 optimal weight: 0.5980 chunk 5 optimal weight: 0.0670 chunk 21 optimal weight: 0.6980 overall best weight: 0.5318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7345 moved from start: 0.2215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 2708 Z= 0.177 Angle : 0.558 8.965 3708 Z= 0.252 Chirality : 0.034 0.105 474 Planarity : 0.003 0.048 402 Dihedral : 3.658 10.492 336 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 3.26 % Allowed : 22.10 % Favored : 74.64 % 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: 2.58 (0.46), residues: 318 helix: 2.00 (0.29), residues: 288 sheet: None (None), residues: 0 loop : -1.14 (1.17), residues: 30 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 39 HIS 0.001 0.000 HIS A 101 PHE 0.007 0.001 PHE A 177 TYR 0.004 0.001 TYR B 41 ARG 0.013 0.001 ARG A 74 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 636 Ramachandran restraints generated. 318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 636 Ramachandran restraints generated. 318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 276 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 35 time to evaluate : 0.288 Fit side-chains REVERT: B 74 ARG cc_start: 0.8114 (mpt-90) cc_final: 0.7855 (ttm170) REVERT: B 147 PHE cc_start: 0.8581 (t80) cc_final: 0.8206 (t80) outliers start: 9 outliers final: 5 residues processed: 43 average time/residue: 0.1547 time to fit residues: 8.0229 Evaluate side-chains 41 residues out of total 276 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 36 time to evaluate : 0.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain B residue 42 ILE Chi-restraints excluded: chain B residue 100 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 15 optimal weight: 0.6980 chunk 2 optimal weight: 0.7980 chunk 24 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 29 optimal weight: 0.3980 chunk 26 optimal weight: 1.9990 chunk 17 optimal weight: 0.7980 chunk 12 optimal weight: 0.6980 chunk 22 optimal weight: 0.9990 chunk 8 optimal weight: 2.9990 chunk 25 optimal weight: 0.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7364 moved from start: 0.2279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 2708 Z= 0.203 Angle : 0.569 8.482 3708 Z= 0.254 Chirality : 0.035 0.134 474 Planarity : 0.003 0.027 402 Dihedral : 3.657 10.302 336 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 2.17 % Allowed : 22.83 % Favored : 75.00 % 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: 2.56 (0.46), residues: 318 helix: 1.99 (0.29), residues: 288 sheet: None (None), residues: 0 loop : -1.19 (1.16), residues: 30 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 131 HIS 0.001 0.000 HIS A 101 PHE 0.008 0.001 PHE A 177 TYR 0.004 0.001 TYR B 41 ARG 0.007 0.001 ARG A 74 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 636 Ramachandran restraints generated. 318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 636 Ramachandran restraints generated. 318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 276 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 37 time to evaluate : 0.277 Fit side-chains REVERT: A 172 LEU cc_start: 0.7835 (tt) cc_final: 0.7276 (mt) REVERT: B 147 PHE cc_start: 0.8575 (t80) cc_final: 0.8184 (t80) REVERT: B 184 MET cc_start: 0.5378 (mmt) cc_final: 0.5100 (tpp) outliers start: 6 outliers final: 5 residues processed: 42 average time/residue: 0.1566 time to fit residues: 7.9501 Evaluate side-chains 42 residues out of total 276 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 37 time to evaluate : 0.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain B residue 42 ILE Chi-restraints excluded: chain B residue 100 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 27 optimal weight: 5.9990 chunk 28 optimal weight: 1.9990 chunk 18 optimal weight: 0.0000 chunk 30 optimal weight: 0.6980 chunk 14 optimal weight: 0.8980 chunk 21 optimal weight: 0.0000 chunk 31 optimal weight: 0.7980 chunk 29 optimal weight: 0.6980 chunk 25 optimal weight: 0.7980 chunk 2 optimal weight: 0.8980 chunk 19 optimal weight: 0.5980 overall best weight: 0.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7317 moved from start: 0.2365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 2708 Z= 0.147 Angle : 0.526 8.843 3708 Z= 0.237 Chirality : 0.034 0.113 474 Planarity : 0.002 0.026 402 Dihedral : 3.515 9.730 336 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 1.45 % Allowed : 24.28 % Favored : 74.28 % 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: 2.86 (0.46), residues: 318 helix: 2.18 (0.29), residues: 288 sheet: None (None), residues: 0 loop : -0.99 (1.19), residues: 30 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 131 HIS 0.001 0.000 HIS A 101 PHE 0.006 0.001 PHE A 177 TYR 0.004 0.001 TYR B 41 ARG 0.010 0.001 ARG A 74 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 636 Ramachandran restraints generated. 318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 636 Ramachandran restraints generated. 318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 276 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 34 time to evaluate : 0.262 Fit side-chains REVERT: B 74 ARG cc_start: 0.8118 (mpt-90) cc_final: 0.7859 (ttm170) REVERT: B 147 PHE cc_start: 0.8540 (t80) cc_final: 0.8170 (t80) outliers start: 4 outliers final: 3 residues processed: 38 average time/residue: 0.1675 time to fit residues: 7.6429 Evaluate side-chains 36 residues out of total 276 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 33 time to evaluate : 0.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain B residue 100 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 15 optimal weight: 0.7980 chunk 20 optimal weight: 0.9980 chunk 27 optimal weight: 4.9990 chunk 7 optimal weight: 0.9990 chunk 23 optimal weight: 0.5980 chunk 3 optimal weight: 0.5980 chunk 25 optimal weight: 0.6980 chunk 10 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 4 optimal weight: 0.9990 chunk 22 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7366 moved from start: 0.2399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 2708 Z= 0.215 Angle : 0.599 9.233 3708 Z= 0.264 Chirality : 0.036 0.112 474 Planarity : 0.002 0.028 402 Dihedral : 3.626 12.540 336 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 1.81 % Allowed : 24.64 % Favored : 73.55 % 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: 2.67 (0.46), residues: 318 helix: 2.05 (0.29), residues: 288 sheet: None (None), residues: 0 loop : -0.99 (1.18), residues: 30 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 39 HIS 0.001 0.000 HIS A 101 PHE 0.008 0.001 PHE A 177 TYR 0.004 0.001 TYR B 125 ARG 0.003 0.001 ARG A 132 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 636 Ramachandran restraints generated. 318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 636 Ramachandran restraints generated. 318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 276 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 34 time to evaluate : 0.283 Fit side-chains REVERT: A 61 MET cc_start: 0.7867 (tpp) cc_final: 0.7448 (tpp) REVERT: A 172 LEU cc_start: 0.7741 (tt) cc_final: 0.7277 (mt) REVERT: B 147 PHE cc_start: 0.8568 (t80) cc_final: 0.8198 (t80) REVERT: B 184 MET cc_start: 0.5902 (tpp) cc_final: 0.5104 (mmm) outliers start: 5 outliers final: 3 residues processed: 38 average time/residue: 0.1667 time to fit residues: 7.6662 Evaluate side-chains 37 residues out of total 276 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 34 time to evaluate : 0.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain B residue 100 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 1 optimal weight: 0.3980 chunk 18 optimal weight: 0.5980 chunk 29 optimal weight: 0.9980 chunk 17 optimal weight: 1.9990 chunk 21 optimal weight: 0.0980 chunk 0 optimal weight: 0.6980 chunk 20 optimal weight: 0.5980 chunk 19 optimal weight: 0.2980 chunk 12 optimal weight: 0.9990 chunk 11 optimal weight: 0.9980 chunk 31 optimal weight: 0.8980 overall best weight: 0.3980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.173199 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.144550 restraints weight = 3096.322| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.148617 restraints weight = 1880.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.151024 restraints weight = 1382.843| |-----------------------------------------------------------------------------| r_work (final): 0.3795 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7346 moved from start: 0.2450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 2708 Z= 0.151 Angle : 0.576 9.772 3708 Z= 0.249 Chirality : 0.034 0.161 474 Planarity : 0.002 0.026 402 Dihedral : 3.506 11.376 336 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 1.81 % Allowed : 24.64 % Favored : 73.55 % 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: 2.91 (0.46), residues: 318 helix: 2.20 (0.29), residues: 288 sheet: None (None), residues: 0 loop : -0.83 (1.21), residues: 30 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 39 HIS 0.001 0.000 HIS A 101 PHE 0.006 0.001 PHE A 177 TYR 0.004 0.001 TYR B 41 ARG 0.003 0.000 ARG A 132 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 917.61 seconds wall clock time: 16 minutes 56.33 seconds (1016.33 seconds total)