Starting phenix.real_space_refine on Thu Dec 7 23:12:57 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f3t_31440/12_2023/7f3t_31440_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f3t_31440/12_2023/7f3t_31440.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.69 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f3t_31440/12_2023/7f3t_31440.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f3t_31440/12_2023/7f3t_31440.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f3t_31440/12_2023/7f3t_31440_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f3t_31440/12_2023/7f3t_31440_updated.pdb" } resolution = 3.69 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= 0.003 sd= 0.107 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: 5 Type Number sf(0) Gaussians P 6 5.49 5 S 34 5.16 5 C 3682 2.51 5 N 934 2.21 5 O 976 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 152": "NH1" <-> "NH2" Residue "A ARG 158": "NH1" <-> "NH2" Residue "A TYR 229": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 235": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 274": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 333": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 152": "NH1" <-> "NH2" Residue "B ARG 158": "NH1" <-> "NH2" Residue "B TYR 229": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 235": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 274": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 333": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 5632 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2768 Number of conformers: 1 Conformer: "" Number of residues, atoms: 330, 2768 Classifications: {'peptide': 330} Link IDs: {'PTRANS': 8, 'TRANS': 321} Chain: "B" Number of atoms: 2768 Number of conformers: 1 Conformer: "" Number of residues, atoms: 330, 2768 Classifications: {'peptide': 330} Link IDs: {'PTRANS': 8, 'TRANS': 321} Chain: "A" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 48 Unusual residues: {'COA': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 48 Unusual residues: {'COA': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.63, per 1000 atoms: 0.64 Number of scatterers: 5632 At special positions: 0 Unit cell: (86.67, 118.77, 93.09, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 34 16.00 P 6 15.00 O 976 8.00 N 934 7.00 C 3682 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: 2.36 Conformation dependent library (CDL) restraints added in 975.0 milliseconds 1312 Ramachandran restraints generated. 656 Oldfield, 0 Emsley, 656 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1252 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 18 helices and 0 sheets defined 80.9% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.04 Creating SS restraints... Processing helix chain 'A' and resid 9 through 69 removed outlier: 3.871A pdb=" N THR A 29 " --> pdb=" O ASN A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 74 through 99 removed outlier: 5.171A pdb=" N ALA A 79 " --> pdb=" O GLU A 75 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N ALA A 80 " --> pdb=" O ALA A 76 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N GLU A 89 " --> pdb=" O ASN A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 111 No H-bonds generated for 'chain 'A' and resid 109 through 111' Processing helix chain 'A' and resid 124 through 153 removed outlier: 4.440A pdb=" N TYR A 129 " --> pdb=" O ALA A 125 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ASP A 131 " --> pdb=" O PHE A 127 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N GLU A 132 " --> pdb=" O ALA A 128 " (cutoff:3.500A) Processing helix chain 'A' and resid 159 through 185 removed outlier: 3.954A pdb=" N CYS A 173 " --> pdb=" O VAL A 169 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N ASN A 184 " --> pdb=" O SER A 180 " (cutoff:3.500A) Processing helix chain 'A' and resid 191 through 209 removed outlier: 4.356A pdb=" N HIS A 196 " --> pdb=" O TRP A 193 " (cutoff:3.500A) Processing helix chain 'A' and resid 220 through 252 removed outlier: 3.808A pdb=" N TYR A 239 " --> pdb=" O PHE A 235 " (cutoff:3.500A) Processing helix chain 'A' and resid 261 through 298 Proline residue: A 277 - end of helix Processing helix chain 'A' and resid 306 through 335 Proline residue: A 313 - end of helix Processing helix chain 'B' and resid 9 through 69 removed outlier: 3.870A pdb=" N THR B 29 " --> pdb=" O ASN B 25 " (cutoff:3.500A) Processing helix chain 'B' and resid 74 through 99 removed outlier: 5.171A pdb=" N ALA B 79 " --> pdb=" O GLU B 75 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N ALA B 80 " --> pdb=" O ALA B 76 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N GLU B 89 " --> pdb=" O ASN B 85 " (cutoff:3.500A) Processing helix chain 'B' and resid 109 through 111 No H-bonds generated for 'chain 'B' and resid 109 through 111' Processing helix chain 'B' and resid 124 through 153 removed outlier: 4.440A pdb=" N TYR B 129 " --> pdb=" O ALA B 125 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ASP B 131 " --> pdb=" O PHE B 127 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N GLU B 132 " --> pdb=" O ALA B 128 " (cutoff:3.500A) Processing helix chain 'B' and resid 159 through 185 removed outlier: 3.954A pdb=" N CYS B 173 " --> pdb=" O VAL B 169 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N ASN B 184 " --> pdb=" O SER B 180 " (cutoff:3.500A) Processing helix chain 'B' and resid 191 through 209 removed outlier: 4.356A pdb=" N HIS B 196 " --> pdb=" O TRP B 193 " (cutoff:3.500A) Processing helix chain 'B' and resid 220 through 252 removed outlier: 3.808A pdb=" N TYR B 239 " --> pdb=" O PHE B 235 " (cutoff:3.500A) Processing helix chain 'B' and resid 261 through 298 Proline residue: B 277 - end of helix Processing helix chain 'B' and resid 306 through 335 Proline residue: B 313 - end of helix 432 hydrogen bonds defined for protein. 1206 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.47 Time building geometry restraints manager: 2.51 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.77: 5738 1.77 - 2.33: 50 2.33 - 2.88: 2 2.88 - 3.43: 0 3.43 - 3.99: 2 Bond restraints: 5792 Sorted by residual: bond pdb=" AO6 COA A1000 " pdb=" AP2 COA A1000 " ideal model delta sigma weight residual 1.610 3.989 -2.379 2.00e-02 2.50e+03 1.42e+04 bond pdb=" AO6 COA B1000 " pdb=" AP2 COA B1000 " ideal model delta sigma weight residual 1.610 3.989 -2.379 2.00e-02 2.50e+03 1.41e+04 bond pdb=" AP1 COA A1000 " pdb="AO5* COA A1000 " ideal model delta sigma weight residual 1.610 2.826 -1.216 2.00e-02 2.50e+03 3.70e+03 bond pdb=" AP1 COA B1000 " pdb="AO5* COA B1000 " ideal model delta sigma weight residual 1.610 2.826 -1.216 2.00e-02 2.50e+03 3.70e+03 bond pdb=" PC9 COA A1000 " pdb=" PO9 COA A1000 " ideal model delta sigma weight residual 1.410 1.217 0.193 2.00e-02 2.50e+03 9.34e+01 ... (remaining 5787 not shown) Histogram of bond angle deviations from ideal: 18.01 - 42.92: 2 42.92 - 67.84: 4 67.84 - 92.76: 0 92.76 - 117.67: 4142 117.67 - 142.59: 3694 Bond angle restraints: 7842 Sorted by residual: angle pdb=" AO3 COA B1000 " pdb=" AP2 COA B1000 " pdb=" AO6 COA B1000 " ideal model delta sigma weight residual 102.60 18.01 84.59 3.00e+00 1.11e-01 7.95e+02 angle pdb=" AO3 COA A1000 " pdb=" AP2 COA A1000 " pdb=" AO6 COA A1000 " ideal model delta sigma weight residual 102.60 18.02 84.58 3.00e+00 1.11e-01 7.95e+02 angle pdb=" AO2 COA B1000 " pdb=" AP1 COA B1000 " pdb="AO5* COA B1000 " ideal model delta sigma weight residual 109.50 64.64 44.86 3.00e+00 1.11e-01 2.24e+02 angle pdb=" AO2 COA A1000 " pdb=" AP1 COA A1000 " pdb="AO5* COA A1000 " ideal model delta sigma weight residual 109.50 64.66 44.84 3.00e+00 1.11e-01 2.23e+02 angle pdb=" AO3 COA B1000 " pdb=" AP1 COA B1000 " pdb="AO5* COA B1000 " ideal model delta sigma weight residual 102.60 62.39 40.21 3.00e+00 1.11e-01 1.80e+02 ... (remaining 7837 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.41: 3232 35.41 - 70.83: 106 70.83 - 106.24: 12 106.24 - 141.66: 0 141.66 - 177.07: 4 Dihedral angle restraints: 3354 sinusoidal: 1414 harmonic: 1940 Sorted by residual: dihedral pdb=" AO3 COA B1000 " pdb=" AP1 COA B1000 " pdb="AO5* COA B1000 " pdb="AC5* COA B1000 " ideal model delta sinusoidal sigma weight residual 291.94 114.87 177.07 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" AO3 COA A1000 " pdb=" AP1 COA A1000 " pdb="AO5* COA A1000 " pdb="AC5* COA A1000 " ideal model delta sinusoidal sigma weight residual 291.94 114.87 177.07 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" AP1 COA A1000 " pdb="AC5* COA A1000 " pdb="AO5* COA A1000 " pdb="AC4* COA A1000 " ideal model delta sinusoidal sigma weight residual 111.68 -82.53 -165.79 1 2.00e+01 2.50e-03 4.73e+01 ... (remaining 3351 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 571 0.054 - 0.108: 193 0.108 - 0.163: 45 0.163 - 0.217: 15 0.217 - 0.271: 2 Chirality restraints: 826 Sorted by residual: chirality pdb="AC3* COA A1000 " pdb="AC2* COA A1000 " pdb="AC4* COA A1000 " pdb="AO3* COA A1000 " both_signs ideal model delta sigma weight residual False -2.47 -2.74 0.27 2.00e-01 2.50e+01 1.83e+00 chirality pdb="AC3* COA B1000 " pdb="AC2* COA B1000 " pdb="AC4* COA B1000 " pdb="AO3* COA B1000 " both_signs ideal model delta sigma weight residual False -2.47 -2.74 0.27 2.00e-01 2.50e+01 1.80e+00 chirality pdb="AC2* COA B1000 " pdb="AC1* COA B1000 " pdb="AC3* COA B1000 " pdb="AO2* COA B1000 " both_signs ideal model delta sigma weight residual False -2.47 -2.69 0.22 2.00e-01 2.50e+01 1.16e+00 ... (remaining 823 not shown) Planarity restraints: 966 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL A 112 " -0.010 2.00e-02 2.50e+03 1.96e-02 3.84e+00 pdb=" C VAL A 112 " 0.034 2.00e-02 2.50e+03 pdb=" O VAL A 112 " -0.013 2.00e-02 2.50e+03 pdb=" N LEU A 113 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL B 112 " 0.010 2.00e-02 2.50e+03 1.95e-02 3.79e+00 pdb=" C VAL B 112 " -0.034 2.00e-02 2.50e+03 pdb=" O VAL B 112 " 0.012 2.00e-02 2.50e+03 pdb=" N LEU B 113 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU A 179 " 0.009 2.00e-02 2.50e+03 1.69e-02 2.85e+00 pdb=" C GLU A 179 " -0.029 2.00e-02 2.50e+03 pdb=" O GLU A 179 " 0.011 2.00e-02 2.50e+03 pdb=" N SER A 180 " 0.010 2.00e-02 2.50e+03 ... (remaining 963 not shown) Histogram of nonbonded interaction distances: 1.60 - 2.26: 12 2.26 - 2.92: 2628 2.92 - 3.58: 8453 3.58 - 4.24: 11813 4.24 - 4.90: 19661 Nonbonded interactions: 42567 Sorted by model distance: nonbonded pdb=" AO6 COA B1000 " pdb=" AP1 COA B1000 " model vdw 1.596 2.720 nonbonded pdb=" AP2 COA B1000 " pdb="AO5* COA B1000 " model vdw 1.596 2.720 nonbonded pdb=" AP2 COA A1000 " pdb="AO5* COA A1000 " model vdw 1.597 2.720 nonbonded pdb=" AO6 COA A1000 " pdb=" AP1 COA A1000 " model vdw 1.597 2.720 nonbonded pdb=" NE2 GLN A 54 " pdb=" OD2 ASP B 22 " model vdw 2.124 2.520 ... (remaining 42562 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model 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=0.00 max=1.00 mean=0.89 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: 1.050 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: 3.770 Check model and map are aligned: 0.090 Set scattering table: 0.060 Process input model: 19.870 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 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 : 0.051 2.379 5792 Z= 3.503 Angle : 2.149 84.591 7842 Z= 0.867 Chirality : 0.061 0.271 826 Planarity : 0.004 0.031 966 Dihedral : 18.385 177.073 2102 Min Nonbonded Distance : 1.596 Molprobity Statistics. All-atom Clashscore : 17.34 Ramachandran Plot: Outliers : 0.30 % Allowed : 5.18 % Favored : 94.51 % Rotamer: Outliers : 0.33 % Allowed : 2.51 % Favored : 97.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.40 (0.32), residues: 656 helix: 0.98 (0.22), residues: 522 sheet: None (None), residues: 0 loop : -2.50 (0.56), residues: 134 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 192 HIS 0.007 0.002 HIS B 196 PHE 0.019 0.002 PHE A 274 TYR 0.024 0.002 TYR B 171 ARG 0.015 0.002 ARG B 14 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1312 Ramachandran restraints generated. 656 Oldfield, 0 Emsley, 656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1312 Ramachandran restraints generated. 656 Oldfield, 0 Emsley, 656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** WARNING: vdw radius undefined for: (HS1 HS); setting to: 1.0 Evaluate side-chains 74 residues out of total 598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 72 time to evaluate : 0.616 Fit side-chains outliers start: 2 outliers final: 0 residues processed: 72 average time/residue: 0.1614 time to fit residues: 16.1343 Evaluate side-chains 61 residues out of total 598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 61 time to evaluate : 0.660 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.9037 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 55 optimal weight: 0.5980 chunk 50 optimal weight: 0.5980 chunk 27 optimal weight: 0.7980 chunk 17 optimal weight: 0.7980 chunk 33 optimal weight: 0.6980 chunk 26 optimal weight: 0.9990 chunk 51 optimal weight: 1.9990 chunk 20 optimal weight: 0.9990 chunk 31 optimal weight: 0.9980 chunk 38 optimal weight: 3.9990 chunk 59 optimal weight: 0.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 237 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7757 moved from start: 0.1562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 5792 Z= 0.200 Angle : 0.770 9.211 7842 Z= 0.387 Chirality : 0.042 0.146 826 Planarity : 0.004 0.028 966 Dihedral : 15.261 178.222 766 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 13.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 2.84 % Allowed : 11.87 % Favored : 85.28 % 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: 1.58 (0.34), residues: 656 helix: 1.72 (0.22), residues: 538 sheet: None (None), residues: 0 loop : -2.14 (0.62), residues: 118 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 285 HIS 0.002 0.001 HIS B 196 PHE 0.009 0.001 PHE B 136 TYR 0.015 0.001 TYR A 238 ARG 0.003 0.001 ARG A 31 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1312 Ramachandran restraints generated. 656 Oldfield, 0 Emsley, 656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1312 Ramachandran restraints generated. 656 Oldfield, 0 Emsley, 656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** WARNING: vdw radius undefined for: (HS1 HS); setting to: 1.0 Evaluate side-chains 102 residues out of total 598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 85 time to evaluate : 0.667 Fit side-chains outliers start: 17 outliers final: 7 residues processed: 93 average time/residue: 0.1657 time to fit residues: 20.6648 Evaluate side-chains 67 residues out of total 598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 60 time to evaluate : 0.628 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0549 time to fit residues: 1.5543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 33 optimal weight: 7.9990 chunk 18 optimal weight: 0.0270 chunk 49 optimal weight: 0.5980 chunk 40 optimal weight: 3.9990 chunk 16 optimal weight: 0.5980 chunk 60 optimal weight: 0.9980 chunk 64 optimal weight: 0.7980 chunk 53 optimal weight: 0.9980 chunk 59 optimal weight: 0.9990 chunk 20 optimal weight: 0.4980 chunk 48 optimal weight: 0.9990 overall best weight: 0.5038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 237 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7714 moved from start: 0.2433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 5792 Z= 0.171 Angle : 0.688 9.672 7842 Z= 0.348 Chirality : 0.039 0.133 826 Planarity : 0.004 0.025 966 Dihedral : 13.760 163.730 766 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 13.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 3.51 % Allowed : 16.22 % Favored : 80.27 % 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: 2.26 (0.34), residues: 656 helix: 2.29 (0.23), residues: 498 sheet: None (None), residues: 0 loop : -1.18 (0.54), residues: 158 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 285 HIS 0.003 0.001 HIS A 196 PHE 0.007 0.001 PHE B 318 TYR 0.012 0.001 TYR B 238 ARG 0.001 0.000 ARG B 178 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1312 Ramachandran restraints generated. 656 Oldfield, 0 Emsley, 656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1312 Ramachandran restraints generated. 656 Oldfield, 0 Emsley, 656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** WARNING: vdw radius undefined for: (HS1 HS); setting to: 1.0 Evaluate side-chains 105 residues out of total 598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 84 time to evaluate : 0.644 Fit side-chains outliers start: 21 outliers final: 5 residues processed: 97 average time/residue: 0.1609 time to fit residues: 21.2017 Evaluate side-chains 80 residues out of total 598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 75 time to evaluate : 0.712 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0566 time to fit residues: 1.4324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 59 optimal weight: 0.8980 chunk 45 optimal weight: 1.9990 chunk 31 optimal weight: 0.8980 chunk 6 optimal weight: 20.0000 chunk 28 optimal weight: 0.5980 chunk 40 optimal weight: 3.9990 chunk 60 optimal weight: 0.9990 chunk 63 optimal weight: 0.9980 chunk 57 optimal weight: 4.9990 chunk 17 optimal weight: 0.2980 chunk 53 optimal weight: 0.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 237 GLN B 237 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7742 moved from start: 0.2719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 5792 Z= 0.200 Angle : 0.706 10.117 7842 Z= 0.357 Chirality : 0.039 0.142 826 Planarity : 0.004 0.025 966 Dihedral : 13.192 157.703 766 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 14.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 3.34 % Allowed : 19.23 % Favored : 77.42 % 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 (0.34), residues: 656 helix: 2.26 (0.23), residues: 506 sheet: None (None), residues: 0 loop : -1.45 (0.54), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 285 HIS 0.004 0.001 HIS B 196 PHE 0.018 0.001 PHE B 127 TYR 0.014 0.001 TYR B 171 ARG 0.003 0.000 ARG B 34 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1312 Ramachandran restraints generated. 656 Oldfield, 0 Emsley, 656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1312 Ramachandran restraints generated. 656 Oldfield, 0 Emsley, 656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** WARNING: vdw radius undefined for: (HS1 HS); setting to: 1.0 Evaluate side-chains 101 residues out of total 598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 81 time to evaluate : 0.633 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 20 outliers final: 11 residues processed: 91 average time/residue: 0.1470 time to fit residues: 18.5035 Evaluate side-chains 83 residues out of total 598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 72 time to evaluate : 0.653 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.0619 time to fit residues: 2.0381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 36 optimal weight: 0.5980 chunk 0 optimal weight: 20.0000 chunk 47 optimal weight: 0.0270 chunk 26 optimal weight: 0.9990 chunk 54 optimal weight: 0.9980 chunk 44 optimal weight: 5.9990 chunk 32 optimal weight: 0.9980 chunk 57 optimal weight: 7.9990 chunk 16 optimal weight: 0.6980 chunk 21 optimal weight: 2.9990 chunk 12 optimal weight: 0.9980 overall best weight: 0.6638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 237 GLN B 237 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7726 moved from start: 0.2990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 5792 Z= 0.193 Angle : 0.711 10.625 7842 Z= 0.355 Chirality : 0.039 0.176 826 Planarity : 0.004 0.025 966 Dihedral : 12.387 147.939 766 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 14.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 1.84 % Allowed : 21.40 % Favored : 76.76 % 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: 2.36 (0.34), residues: 656 helix: 2.37 (0.23), residues: 500 sheet: None (None), residues: 0 loop : -1.23 (0.51), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 285 HIS 0.003 0.001 HIS B 196 PHE 0.015 0.001 PHE B 127 TYR 0.013 0.001 TYR B 171 ARG 0.002 0.000 ARG B 34 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1312 Ramachandran restraints generated. 656 Oldfield, 0 Emsley, 656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1312 Ramachandran restraints generated. 656 Oldfield, 0 Emsley, 656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** WARNING: vdw radius undefined for: (HS1 HS); setting to: 1.0 Evaluate side-chains 82 residues out of total 598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 71 time to evaluate : 0.665 Fit side-chains outliers start: 11 outliers final: 3 residues processed: 76 average time/residue: 0.1381 time to fit residues: 15.0448 Evaluate side-chains 67 residues out of total 598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 64 time to evaluate : 0.658 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0577 time to fit residues: 1.2142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 37 optimal weight: 7.9990 chunk 15 optimal weight: 0.9980 chunk 63 optimal weight: 2.9990 chunk 53 optimal weight: 0.6980 chunk 29 optimal weight: 0.7980 chunk 5 optimal weight: 0.9990 chunk 21 optimal weight: 0.1980 chunk 33 optimal weight: 7.9990 chunk 61 optimal weight: 0.9990 chunk 7 optimal weight: 0.9990 chunk 36 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 237 GLN B 237 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7741 moved from start: 0.3157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 5792 Z= 0.200 Angle : 0.723 14.311 7842 Z= 0.354 Chirality : 0.039 0.170 826 Planarity : 0.004 0.056 966 Dihedral : 11.922 141.523 766 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 13.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 1.67 % Allowed : 21.40 % Favored : 76.92 % 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: 2.31 (0.33), residues: 656 helix: 2.35 (0.23), residues: 504 sheet: None (None), residues: 0 loop : -1.43 (0.51), residues: 152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 285 HIS 0.004 0.001 HIS B 196 PHE 0.013 0.001 PHE A 127 TYR 0.014 0.001 TYR A 171 ARG 0.011 0.000 ARG B 14 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1312 Ramachandran restraints generated. 656 Oldfield, 0 Emsley, 656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1312 Ramachandran restraints generated. 656 Oldfield, 0 Emsley, 656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** WARNING: vdw radius undefined for: (HS1 HS); setting to: 1.0 Evaluate side-chains 81 residues out of total 598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 71 time to evaluate : 0.712 Fit side-chains outliers start: 10 outliers final: 1 residues processed: 78 average time/residue: 0.1496 time to fit residues: 16.3015 Evaluate side-chains 65 residues out of total 598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 64 time to evaluate : 0.666 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0515 time to fit residues: 1.0069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 46 optimal weight: 0.9980 chunk 36 optimal weight: 0.7980 chunk 53 optimal weight: 0.0170 chunk 35 optimal weight: 0.7980 chunk 63 optimal weight: 0.6980 chunk 39 optimal weight: 0.0010 chunk 38 optimal weight: 1.9990 chunk 29 optimal weight: 0.0870 chunk 25 optimal weight: 6.9990 chunk 37 optimal weight: 0.9980 chunk 19 optimal weight: 0.7980 overall best weight: 0.3202 ------------------------------------------------------------------------------- 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: 0.7650 moved from start: 0.3702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 5792 Z= 0.169 Angle : 0.734 12.358 7842 Z= 0.366 Chirality : 0.040 0.223 826 Planarity : 0.004 0.031 966 Dihedral : 11.046 125.685 766 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 13.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 1.84 % Allowed : 21.57 % Favored : 76.59 % 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: 2.48 (0.34), residues: 656 helix: 2.46 (0.23), residues: 506 sheet: None (None), residues: 0 loop : -1.35 (0.50), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 16 HIS 0.002 0.000 HIS A 283 PHE 0.024 0.001 PHE B 23 TYR 0.010 0.001 TYR A 238 ARG 0.008 0.000 ARG B 14 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1312 Ramachandran restraints generated. 656 Oldfield, 0 Emsley, 656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1312 Ramachandran restraints generated. 656 Oldfield, 0 Emsley, 656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** WARNING: vdw radius undefined for: (HS1 HS); setting to: 1.0 Evaluate side-chains 88 residues out of total 598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 77 time to evaluate : 0.597 Fit side-chains outliers start: 11 outliers final: 5 residues processed: 84 average time/residue: 0.1533 time to fit residues: 17.8947 Evaluate side-chains 70 residues out of total 598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 65 time to evaluate : 0.674 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0587 time to fit residues: 1.4522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 12 optimal weight: 0.5980 chunk 40 optimal weight: 6.9990 chunk 43 optimal weight: 0.6980 chunk 31 optimal weight: 0.5980 chunk 5 optimal weight: 0.9980 chunk 50 optimal weight: 2.9990 chunk 57 optimal weight: 6.9990 chunk 60 optimal weight: 0.9980 chunk 55 optimal weight: 0.9980 chunk 59 optimal weight: 0.9980 chunk 35 optimal weight: 0.6980 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: 0.7741 moved from start: 0.3614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 5792 Z= 0.217 Angle : 0.765 11.568 7842 Z= 0.381 Chirality : 0.040 0.247 826 Planarity : 0.004 0.037 966 Dihedral : 7.570 59.405 766 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 14.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 0.33 % Allowed : 23.75 % Favored : 75.92 % 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: 2.45 (0.33), residues: 656 helix: 2.44 (0.23), residues: 506 sheet: None (None), residues: 0 loop : -1.35 (0.50), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 16 HIS 0.004 0.001 HIS B 196 PHE 0.023 0.001 PHE B 23 TYR 0.016 0.001 TYR A 171 ARG 0.007 0.000 ARG B 14 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1312 Ramachandran restraints generated. 656 Oldfield, 0 Emsley, 656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1312 Ramachandran restraints generated. 656 Oldfield, 0 Emsley, 656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** WARNING: vdw radius undefined for: (HS1 HS); setting to: 1.0 Evaluate side-chains 70 residues out of total 598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 68 time to evaluate : 0.691 Fit side-chains outliers start: 2 outliers final: 0 residues processed: 70 average time/residue: 0.1242 time to fit residues: 12.9396 Evaluate side-chains 62 residues out of total 598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 62 time to evaluate : 0.641 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.9170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 25 optimal weight: 0.1980 chunk 46 optimal weight: 0.4980 chunk 18 optimal weight: 0.7980 chunk 53 optimal weight: 0.4980 chunk 56 optimal weight: 0.5980 chunk 59 optimal weight: 5.9990 chunk 38 optimal weight: 0.9990 chunk 62 optimal weight: 0.9990 chunk 29 optimal weight: 0.0050 chunk 43 optimal weight: 0.9990 chunk 65 optimal weight: 8.9990 overall best weight: 0.3594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 184 ASN B 184 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7663 moved from start: 0.4013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 5792 Z= 0.193 Angle : 0.736 11.260 7842 Z= 0.370 Chirality : 0.038 0.224 826 Planarity : 0.004 0.026 966 Dihedral : 7.148 58.509 766 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 14.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 0.67 % Allowed : 24.25 % Favored : 75.08 % 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: 2.57 (0.33), residues: 656 helix: 2.53 (0.23), residues: 506 sheet: None (None), residues: 0 loop : -1.36 (0.48), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 192 HIS 0.002 0.000 HIS A 283 PHE 0.023 0.001 PHE B 23 TYR 0.009 0.001 TYR A 238 ARG 0.006 0.000 ARG B 14 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1312 Ramachandran restraints generated. 656 Oldfield, 0 Emsley, 656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1312 Ramachandran restraints generated. 656 Oldfield, 0 Emsley, 656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** WARNING: vdw radius undefined for: (HS1 HS); setting to: 1.0 Evaluate side-chains 67 residues out of total 598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 63 time to evaluate : 0.585 Fit side-chains outliers start: 4 outliers final: 2 residues processed: 65 average time/residue: 0.1276 time to fit residues: 12.2228 Evaluate side-chains 65 residues out of total 598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 63 time to evaluate : 0.693 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0724 time to fit residues: 1.1556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 60 optimal weight: 0.9990 chunk 52 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 chunk 32 optimal weight: 10.0000 chunk 41 optimal weight: 0.9980 chunk 55 optimal weight: 0.8980 chunk 16 optimal weight: 0.6980 chunk 48 optimal weight: 0.9980 chunk 7 optimal weight: 0.0000 chunk 14 optimal weight: 2.9990 overall best weight: 0.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7729 moved from start: 0.3858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.081 5792 Z= 0.226 Angle : 0.759 12.002 7842 Z= 0.385 Chirality : 0.039 0.211 826 Planarity : 0.004 0.027 966 Dihedral : 7.019 58.021 766 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 13.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 0.33 % Allowed : 25.08 % Favored : 74.58 % 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: 2.52 (0.33), residues: 656 helix: 2.49 (0.23), residues: 506 sheet: None (None), residues: 0 loop : -1.36 (0.49), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 193 HIS 0.003 0.001 HIS A 196 PHE 0.023 0.001 PHE B 23 TYR 0.015 0.001 TYR A 171 ARG 0.006 0.000 ARG B 14 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1312 Ramachandran restraints generated. 656 Oldfield, 0 Emsley, 656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1312 Ramachandran restraints generated. 656 Oldfield, 0 Emsley, 656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** WARNING: vdw radius undefined for: (HS1 HS); setting to: 1.0 Evaluate side-chains 64 residues out of total 598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 62 time to evaluate : 0.667 Fit side-chains outliers start: 2 outliers final: 0 residues processed: 64 average time/residue: 0.1271 time to fit residues: 12.1677 Evaluate side-chains 61 residues out of total 598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 61 time to evaluate : 0.659 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.9245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 52 optimal weight: 0.9990 chunk 21 optimal weight: 0.6980 chunk 53 optimal weight: 0.1980 chunk 6 optimal weight: 20.0000 chunk 9 optimal weight: 1.9990 chunk 46 optimal weight: 0.5980 chunk 2 optimal weight: 1.9990 chunk 37 optimal weight: 5.9990 chunk 60 optimal weight: 0.9980 chunk 35 optimal weight: 0.7980 chunk 44 optimal weight: 1.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 117 ASN B 117 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.150504 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.107390 restraints weight = 7524.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.109904 restraints weight = 4828.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.111413 restraints weight = 3829.316| |-----------------------------------------------------------------------------| r_work (final): 0.3319 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7741 moved from start: 0.3947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.085 5792 Z= 0.223 Angle : 0.780 15.479 7842 Z= 0.392 Chirality : 0.039 0.205 826 Planarity : 0.004 0.024 966 Dihedral : 6.989 58.156 766 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 14.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 1.00 % Allowed : 25.08 % Favored : 73.91 % 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: 2.49 (0.33), residues: 656 helix: 2.48 (0.23), residues: 506 sheet: None (None), residues: 0 loop : -1.41 (0.48), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 193 HIS 0.003 0.001 HIS A 283 PHE 0.023 0.001 PHE B 23 TYR 0.013 0.001 TYR A 171 ARG 0.005 0.000 ARG B 14 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1294.70 seconds wall clock time: 24 minutes 14.81 seconds (1454.81 seconds total)