Starting phenix.real_space_refine on Mon Sep 23 11:31:25 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w3t_32293/09_2024/7w3t_32293.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w3t_32293/09_2024/7w3t_32293.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.59 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w3t_32293/09_2024/7w3t_32293.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w3t_32293/09_2024/7w3t_32293.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w3t_32293/09_2024/7w3t_32293.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w3t_32293/09_2024/7w3t_32293.cif" } resolution = 3.59 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.012 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 3 5.16 5 C 915 2.51 5 N 241 2.21 5 O 296 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 1455 Number of models: 1 Model: "" Number of chains: 3 Chain: "B" Number of atoms: 1360 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1360 Classifications: {'peptide': 176} Link IDs: {'PTRANS': 13, 'TRANS': 162} Chain: "A" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "B" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 1.78, per 1000 atoms: 1.22 Number of scatterers: 1455 At special positions: 0 Unit cell: (66.843, 46.684, 55.172, 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 3 16.00 O 296 8.00 N 241 7.00 C 915 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS B 60 " - pdb=" SG CYS B 67 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG A 1 " - " NAG A 2 " " NAG A 2 " - " BMA A 3 " NAG-ASN " NAG A 1 " - " ASN B 186 " " NAG B1000 " - " ASN B 82 " " NAG B1001 " - " ASN B 106 " " NAG B1002 " - " ASN B 117 " " NAG B1003 " - " ASN B 152 " Time building additional restraints: 0.48 Conformation dependent library (CDL) restraints added in 166.0 milliseconds 348 Ramachandran restraints generated. 174 Oldfield, 0 Emsley, 174 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 330 Finding SS restraints... Secondary structure from input PDB file: 7 helices and 3 sheets defined 27.8% alpha, 13.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.21 Creating SS restraints... Processing helix chain 'B' and resid 29 through 41 Processing helix chain 'B' and resid 90 through 94 removed outlier: 3.574A pdb=" N GLN B 93 " --> pdb=" O GLN B 90 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N LEU B 94 " --> pdb=" O LEU B 91 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 90 through 94' Processing helix chain 'B' and resid 112 through 118 removed outlier: 3.819A pdb=" N LEU B 115 " --> pdb=" O PRO B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 136 through 142 removed outlier: 3.501A pdb=" N LEU B 142 " --> pdb=" O LEU B 139 " (cutoff:3.500A) Processing helix chain 'B' and resid 161 through 166 removed outlier: 3.565A pdb=" N VAL B 166 " --> pdb=" O LEU B 163 " (cutoff:3.500A) Processing helix chain 'B' and resid 186 through 191 removed outlier: 3.503A pdb=" N PHE B 189 " --> pdb=" O ASN B 186 " (cutoff:3.500A) Processing helix chain 'B' and resid 193 through 197 Processing sheet with id=AA1, first strand: chain 'B' and resid 42 through 43 removed outlier: 5.402A pdb=" N GLY B 85 " --> pdb=" O SER B 108 " (cutoff:3.500A) removed outlier: 5.162A pdb=" N ILE B 107 " --> pdb=" O ARG B 130 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 65 through 66 removed outlier: 6.383A pdb=" N VAL B 76 " --> pdb=" O GLU B 101 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N LEU B 100 " --> pdb=" O ASP B 125 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N LEU B 124 " --> pdb=" O ARG B 149 " (cutoff:3.500A) removed outlier: 8.061A pdb=" N ASN B 151 " --> pdb=" O LEU B 124 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LEU B 148 " --> pdb=" O VAL B 171 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N SER B 175 " --> pdb=" O LEU B 150 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 157 through 158 removed outlier: 6.452A pdb=" N GLY B 157 " --> pdb=" O THR B 180 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 27 hydrogen bonds defined for protein. 39 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: 0.33 Time building geometry restraints manager: 0.54 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: 475 1.34 - 1.46: 267 1.46 - 1.57: 735 1.57 - 1.69: 0 1.69 - 1.81: 4 Bond restraints: 1481 Sorted by residual: bond pdb=" C1 NAG B1001 " pdb=" O5 NAG B1001 " ideal model delta sigma weight residual 1.406 1.439 -0.033 2.00e-02 2.50e+03 2.75e+00 bond pdb=" C1 NAG A 1 " pdb=" O5 NAG A 1 " ideal model delta sigma weight residual 1.406 1.433 -0.027 2.00e-02 2.50e+03 1.85e+00 bond pdb=" C1 BMA A 3 " pdb=" C2 BMA A 3 " ideal model delta sigma weight residual 1.519 1.545 -0.026 2.00e-02 2.50e+03 1.65e+00 bond pdb=" C1 NAG B1003 " pdb=" O5 NAG B1003 " ideal model delta sigma weight residual 1.406 1.431 -0.025 2.00e-02 2.50e+03 1.55e+00 bond pdb=" C1 NAG B1000 " pdb=" O5 NAG B1000 " ideal model delta sigma weight residual 1.406 1.430 -0.024 2.00e-02 2.50e+03 1.46e+00 ... (remaining 1476 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.43: 1908 1.43 - 2.86: 103 2.86 - 4.29: 10 4.29 - 5.72: 6 5.72 - 7.15: 2 Bond angle restraints: 2029 Sorted by residual: angle pdb=" CA PRO B 134 " pdb=" C PRO B 134 " pdb=" N ILE B 135 " ideal model delta sigma weight residual 114.74 116.95 -2.21 1.03e+00 9.43e-01 4.62e+00 angle pdb=" C3 BMA A 3 " pdb=" C2 BMA A 3 " pdb=" O2 BMA A 3 " ideal model delta sigma weight residual 112.95 106.58 6.37 3.00e+00 1.11e-01 4.50e+00 angle pdb=" CA LEU B 162 " pdb=" CB LEU B 162 " pdb=" CG LEU B 162 " ideal model delta sigma weight residual 116.30 123.45 -7.15 3.50e+00 8.16e-02 4.17e+00 angle pdb=" CA CYS B 60 " pdb=" CB CYS B 60 " pdb=" SG CYS B 60 " ideal model delta sigma weight residual 114.40 109.82 4.58 2.30e+00 1.89e-01 3.96e+00 angle pdb=" C LYS B 144 " pdb=" N LEU B 145 " pdb=" CA LEU B 145 " ideal model delta sigma weight residual 122.74 119.46 3.28 1.82e+00 3.02e-01 3.26e+00 ... (remaining 2024 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.50: 897 21.50 - 43.00: 71 43.00 - 64.50: 8 64.50 - 86.00: 8 86.00 - 107.50: 4 Dihedral angle restraints: 988 sinusoidal: 480 harmonic: 508 Sorted by residual: dihedral pdb=" CB CYS B 60 " pdb=" SG CYS B 60 " pdb=" SG CYS B 67 " pdb=" CB CYS B 67 " ideal model delta sinusoidal sigma weight residual 93.00 132.69 -39.69 1 1.00e+01 1.00e-02 2.21e+01 dihedral pdb=" O4 BMA A 3 " pdb=" C4 BMA A 3 " pdb=" C5 BMA A 3 " pdb=" O5 BMA A 3 " ideal model delta sinusoidal sigma weight residual -71.29 -178.79 107.50 1 3.00e+01 1.11e-03 1.39e+01 dihedral pdb=" C3 BMA A 3 " pdb=" C4 BMA A 3 " pdb=" C5 BMA A 3 " pdb=" O5 BMA A 3 " ideal model delta sinusoidal sigma weight residual 47.62 -57.71 105.33 1 3.00e+01 1.11e-03 1.35e+01 ... (remaining 985 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 209 0.055 - 0.110: 44 0.110 - 0.165: 7 0.165 - 0.220: 3 0.220 - 0.275: 1 Chirality restraints: 264 Sorted by residual: chirality pdb=" C5 BMA A 3 " pdb=" C4 BMA A 3 " pdb=" C6 BMA A 3 " pdb=" O5 BMA A 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.55 0.27 2.00e-01 2.50e+01 1.89e+00 chirality pdb=" C1 NAG B1000 " pdb=" ND2 ASN B 82 " pdb=" C2 NAG B1000 " pdb=" O5 NAG B1000 " both_signs ideal model delta sigma weight residual False -2.40 -2.22 -0.18 2.00e-01 2.50e+01 7.94e-01 chirality pdb=" C1 NAG B1001 " pdb=" ND2 ASN B 106 " pdb=" C2 NAG B1001 " pdb=" O5 NAG B1001 " both_signs ideal model delta sigma weight residual False -2.40 -2.22 -0.18 2.00e-01 2.50e+01 7.86e-01 ... (remaining 261 not shown) Planarity restraints: 263 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP B 62 " 0.018 2.00e-02 2.50e+03 1.86e-02 8.63e+00 pdb=" CG TRP B 62 " -0.049 2.00e-02 2.50e+03 pdb=" CD1 TRP B 62 " 0.025 2.00e-02 2.50e+03 pdb=" CD2 TRP B 62 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP B 62 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP B 62 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP B 62 " 0.004 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 62 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 62 " 0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP B 62 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE B 159 " -0.026 5.00e-02 4.00e+02 4.03e-02 2.60e+00 pdb=" N PRO B 160 " 0.070 5.00e-02 4.00e+02 pdb=" CA PRO B 160 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO B 160 " -0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN B 58 " -0.026 5.00e-02 4.00e+02 3.97e-02 2.53e+00 pdb=" N PRO B 59 " 0.069 5.00e-02 4.00e+02 pdb=" CA PRO B 59 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO B 59 " -0.022 5.00e-02 4.00e+02 ... (remaining 260 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 321 2.79 - 3.32: 1407 3.32 - 3.84: 2237 3.84 - 4.37: 2594 4.37 - 4.90: 4242 Nonbonded interactions: 10801 Sorted by model distance: nonbonded pdb=" OD1 ASN B 68 " pdb=" OG SER B 72 " model vdw 2.259 3.040 nonbonded pdb=" O LEU B 162 " pdb=" OG1 THR B 165 " model vdw 2.278 3.040 nonbonded pdb=" O GLY B 187 " pdb=" OG SER B 190 " model vdw 2.338 3.040 nonbonded pdb=" O LEU B 145 " pdb=" OG SER B 168 " model vdw 2.366 3.040 nonbonded pdb=" O GLY B 85 " pdb=" N SER B 108 " model vdw 2.389 3.120 ... (remaining 10796 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 0.640 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.060 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 9.810 Find NCS groups from input model: 0.020 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:3.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7335 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 : 0.004 0.033 1481 Z= 0.256 Angle : 0.731 7.147 2029 Z= 0.335 Chirality : 0.052 0.275 264 Planarity : 0.006 0.040 258 Dihedral : 17.978 107.496 655 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.83 (0.63), residues: 174 helix: -2.58 (0.70), residues: 44 sheet: -2.90 (0.90), residues: 28 loop : -1.17 (0.65), residues: 102 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.006 TRP B 62 HIS 0.001 0.001 HIS B 64 PHE 0.007 0.001 PHE B 147 TYR 0.012 0.002 TYR B 127 ARG 0.001 0.000 ARG B 130 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 348 Ramachandran restraints generated. 174 Oldfield, 0 Emsley, 174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 348 Ramachandran restraints generated. 174 Oldfield, 0 Emsley, 174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 41 time to evaluate : 0.157 Fit side-chains revert: symmetry clash REVERT: B 41 ASN cc_start: 0.8180 (m110) cc_final: 0.7686 (t0) outliers start: 0 outliers final: 0 residues processed: 41 average time/residue: 0.1139 time to fit residues: 5.4327 Evaluate side-chains 42 residues out of total 160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 42 time to evaluate : 0.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 17 random chunks: chunk 14 optimal weight: 0.9990 chunk 12 optimal weight: 0.9980 chunk 7 optimal weight: 0.8980 chunk 4 optimal weight: 0.7980 chunk 8 optimal weight: 0.8980 chunk 6 optimal weight: 0.0370 chunk 13 optimal weight: 1.9990 chunk 5 optimal weight: 0.6980 chunk 9 optimal weight: 0.5980 chunk 15 optimal weight: 0.0010 chunk 10 optimal weight: 0.6980 overall best weight: 0.4064 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 151 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7379 moved from start: 0.0985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 1481 Z= 0.265 Angle : 0.708 9.049 2029 Z= 0.331 Chirality : 0.051 0.209 264 Planarity : 0.005 0.035 258 Dihedral : 11.465 56.595 329 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.05 % Favored : 91.95 % Rotamer: Outliers : 0.62 % Allowed : 14.38 % Favored : 85.00 % 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: -2.93 (0.62), residues: 174 helix: -2.73 (0.70), residues: 44 sheet: -2.77 (0.88), residues: 29 loop : -1.24 (0.64), residues: 101 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.003 TRP B 62 HIS 0.003 0.002 HIS B 64 PHE 0.013 0.002 PHE B 147 TYR 0.013 0.002 TYR B 103 ARG 0.003 0.001 ARG B 149 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 348 Ramachandran restraints generated. 174 Oldfield, 0 Emsley, 174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 348 Ramachandran restraints generated. 174 Oldfield, 0 Emsley, 174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 43 time to evaluate : 0.136 Fit side-chains revert: symmetry clash REVERT: B 41 ASN cc_start: 0.8195 (m110) cc_final: 0.7624 (t0) REVERT: B 127 TYR cc_start: 0.8715 (p90) cc_final: 0.8456 (p90) REVERT: B 161 MET cc_start: 0.5743 (mmp) cc_final: 0.5393 (mmp) outliers start: 1 outliers final: 1 residues processed: 43 average time/residue: 0.0881 time to fit residues: 4.4776 Evaluate side-chains 43 residues out of total 160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 42 time to evaluate : 0.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 145 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 17 random chunks: chunk 4 optimal weight: 0.9980 chunk 15 optimal weight: 0.8980 chunk 16 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 5 optimal weight: 0.5980 chunk 12 optimal weight: 0.9980 chunk 11 optimal weight: 0.7980 chunk 8 optimal weight: 0.3980 chunk 1 optimal weight: 0.6980 chunk 7 optimal weight: 0.6980 chunk 10 optimal weight: 0.6980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 151 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7416 moved from start: 0.1342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 1481 Z= 0.358 Angle : 0.720 7.187 2029 Z= 0.350 Chirality : 0.053 0.228 264 Planarity : 0.006 0.043 258 Dihedral : 9.000 52.768 329 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.20 % Favored : 90.80 % Rotamer: Outliers : 2.50 % Allowed : 17.50 % Favored : 80.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.11 (0.62), residues: 174 helix: -2.96 (0.68), residues: 44 sheet: -2.81 (0.89), residues: 29 loop : -1.32 (0.64), residues: 101 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.003 TRP B 62 HIS 0.004 0.002 HIS B 64 PHE 0.015 0.002 PHE B 147 TYR 0.014 0.003 TYR B 103 ARG 0.002 0.000 ARG B 149 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 348 Ramachandran restraints generated. 174 Oldfield, 0 Emsley, 174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 348 Ramachandran restraints generated. 174 Oldfield, 0 Emsley, 174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 42 time to evaluate : 0.166 Fit side-chains revert: symmetry clash REVERT: B 41 ASN cc_start: 0.8247 (m110) cc_final: 0.7675 (t0) REVERT: B 127 TYR cc_start: 0.8818 (p90) cc_final: 0.8478 (p90) REVERT: B 161 MET cc_start: 0.5766 (mmp) cc_final: 0.5337 (mmp) outliers start: 4 outliers final: 2 residues processed: 44 average time/residue: 0.1012 time to fit residues: 5.2219 Evaluate side-chains 44 residues out of total 160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 42 time to evaluate : 0.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 145 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 17 random chunks: chunk 15 optimal weight: 0.6980 chunk 16 optimal weight: 0.7980 chunk 8 optimal weight: 0.3980 chunk 14 optimal weight: 0.4980 chunk 4 optimal weight: 0.9990 chunk 13 optimal weight: 0.9980 chunk 9 optimal weight: 0.6980 chunk 0 optimal weight: 0.0980 chunk 12 optimal weight: 0.1980 chunk 6 optimal weight: 0.0970 chunk 11 optimal weight: 0.7980 overall best weight: 0.2578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 151 ASN ** B 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7376 moved from start: 0.1439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 1481 Z= 0.209 Angle : 0.642 5.967 2029 Z= 0.319 Chirality : 0.050 0.219 264 Planarity : 0.005 0.036 258 Dihedral : 7.345 53.715 329 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 0.00 % Allowed : 20.62 % Favored : 79.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.01 (0.63), residues: 174 helix: -2.73 (0.71), residues: 44 sheet: -2.98 (0.95), residues: 27 loop : -1.32 (0.63), residues: 103 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 62 HIS 0.002 0.001 HIS B 64 PHE 0.009 0.002 PHE B 147 TYR 0.008 0.002 TYR B 103 ARG 0.001 0.000 ARG B 149 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 348 Ramachandran restraints generated. 174 Oldfield, 0 Emsley, 174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 348 Ramachandran restraints generated. 174 Oldfield, 0 Emsley, 174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 39 time to evaluate : 0.166 Fit side-chains revert: symmetry clash REVERT: B 41 ASN cc_start: 0.8160 (m110) cc_final: 0.7642 (t0) REVERT: B 127 TYR cc_start: 0.8758 (p90) cc_final: 0.8413 (p90) REVERT: B 161 MET cc_start: 0.5772 (mmp) cc_final: 0.5245 (mmp) outliers start: 0 outliers final: 0 residues processed: 39 average time/residue: 0.1090 time to fit residues: 5.0669 Evaluate side-chains 39 residues out of total 160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 39 time to evaluate : 0.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 17 random chunks: chunk 0 optimal weight: 0.9990 chunk 8 optimal weight: 0.5980 chunk 14 optimal weight: 0.9980 chunk 4 optimal weight: 0.9990 chunk 5 optimal weight: 0.7980 chunk 3 optimal weight: 0.7980 chunk 9 optimal weight: 0.6980 chunk 16 optimal weight: 0.0970 chunk 13 optimal weight: 1.9990 chunk 7 optimal weight: 0.5980 chunk 1 optimal weight: 0.8980 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 151 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7414 moved from start: 0.1627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 1481 Z= 0.334 Angle : 0.675 6.182 2029 Z= 0.336 Chirality : 0.051 0.222 264 Planarity : 0.005 0.033 258 Dihedral : 7.154 53.328 329 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.77 % Favored : 90.23 % Rotamer: Outliers : 1.25 % Allowed : 20.62 % Favored : 78.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.10 (0.63), residues: 174 helix: -2.98 (0.67), residues: 44 sheet: -2.96 (0.96), residues: 27 loop : -1.31 (0.65), residues: 103 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.003 TRP B 62 HIS 0.003 0.002 HIS B 64 PHE 0.014 0.002 PHE B 147 TYR 0.013 0.003 TYR B 103 ARG 0.002 0.000 ARG B 149 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 348 Ramachandran restraints generated. 174 Oldfield, 0 Emsley, 174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 348 Ramachandran restraints generated. 174 Oldfield, 0 Emsley, 174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 40 time to evaluate : 0.159 Fit side-chains REVERT: B 41 ASN cc_start: 0.8203 (m110) cc_final: 0.7668 (t0) REVERT: B 127 TYR cc_start: 0.8785 (p90) cc_final: 0.8392 (p90) REVERT: B 161 MET cc_start: 0.5883 (mmp) cc_final: 0.5365 (mmp) outliers start: 2 outliers final: 2 residues processed: 40 average time/residue: 0.1083 time to fit residues: 5.0707 Evaluate side-chains 42 residues out of total 160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 40 time to evaluate : 0.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 145 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 17 random chunks: chunk 5 optimal weight: 0.9980 chunk 8 optimal weight: 0.8980 chunk 15 optimal weight: 0.9980 chunk 1 optimal weight: 0.3980 chunk 9 optimal weight: 0.9990 chunk 12 optimal weight: 0.8980 chunk 13 optimal weight: 0.9980 chunk 16 optimal weight: 0.6980 chunk 10 optimal weight: 0.8980 chunk 7 optimal weight: 0.6980 chunk 6 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 151 ASN B 178 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7429 moved from start: 0.1787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 1481 Z= 0.381 Angle : 0.705 6.340 2029 Z= 0.349 Chirality : 0.053 0.247 264 Planarity : 0.005 0.034 258 Dihedral : 7.117 53.433 329 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 10.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.77 % Favored : 90.23 % Rotamer: Outliers : 1.88 % Allowed : 20.62 % Favored : 77.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.24 (0.62), residues: 174 helix: -3.15 (0.64), residues: 44 sheet: -3.30 (0.93), residues: 26 loop : -1.32 (0.63), residues: 104 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.004 TRP B 62 HIS 0.004 0.003 HIS B 64 PHE 0.016 0.002 PHE B 147 TYR 0.014 0.003 TYR B 103 ARG 0.002 0.001 ARG B 149 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 348 Ramachandran restraints generated. 174 Oldfield, 0 Emsley, 174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 348 Ramachandran restraints generated. 174 Oldfield, 0 Emsley, 174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 40 time to evaluate : 0.166 Fit side-chains revert: symmetry clash REVERT: B 41 ASN cc_start: 0.8215 (m110) cc_final: 0.7682 (t0) REVERT: B 127 TYR cc_start: 0.8782 (p90) cc_final: 0.8423 (p90) REVERT: B 161 MET cc_start: 0.5935 (mmp) cc_final: 0.5420 (mmp) REVERT: B 162 LEU cc_start: 0.7671 (OUTLIER) cc_final: 0.7395 (tt) outliers start: 3 outliers final: 2 residues processed: 41 average time/residue: 0.1078 time to fit residues: 5.1887 Evaluate side-chains 42 residues out of total 160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 39 time to evaluate : 0.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 162 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 17 random chunks: chunk 9 optimal weight: 0.9980 chunk 4 optimal weight: 0.9980 chunk 3 optimal weight: 0.4980 chunk 10 optimal weight: 0.8980 chunk 11 optimal weight: 0.9980 chunk 8 optimal weight: 0.7980 chunk 1 optimal weight: 0.7980 chunk 12 optimal weight: 0.9980 chunk 14 optimal weight: 0.2980 chunk 15 optimal weight: 0.9980 chunk 6 optimal weight: 0.6980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 151 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7429 moved from start: 0.1871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 1481 Z= 0.357 Angle : 0.693 6.598 2029 Z= 0.345 Chirality : 0.052 0.243 264 Planarity : 0.005 0.035 258 Dihedral : 7.088 53.710 329 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 10.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.34 % Favored : 89.66 % Rotamer: Outliers : 3.12 % Allowed : 21.25 % Favored : 75.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.27 (0.62), residues: 174 helix: -3.15 (0.64), residues: 44 sheet: -3.25 (0.95), residues: 26 loop : -1.36 (0.63), residues: 104 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.004 TRP B 62 HIS 0.004 0.002 HIS B 64 PHE 0.015 0.002 PHE B 147 TYR 0.013 0.003 TYR B 103 ARG 0.002 0.000 ARG B 149 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 348 Ramachandran restraints generated. 174 Oldfield, 0 Emsley, 174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 348 Ramachandran restraints generated. 174 Oldfield, 0 Emsley, 174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 39 time to evaluate : 0.166 Fit side-chains revert: symmetry clash REVERT: B 41 ASN cc_start: 0.8210 (m110) cc_final: 0.7678 (t0) REVERT: B 127 TYR cc_start: 0.8771 (p90) cc_final: 0.8521 (p90) REVERT: B 129 ASN cc_start: 0.7905 (m-40) cc_final: 0.7644 (t0) REVERT: B 161 MET cc_start: 0.5968 (mmp) cc_final: 0.5468 (mmp) REVERT: B 162 LEU cc_start: 0.7655 (OUTLIER) cc_final: 0.7378 (tt) outliers start: 5 outliers final: 3 residues processed: 41 average time/residue: 0.1090 time to fit residues: 5.2779 Evaluate side-chains 43 residues out of total 160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 39 time to evaluate : 0.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 162 LEU Chi-restraints excluded: chain B residue 191 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 17 random chunks: chunk 11 optimal weight: 0.0980 chunk 4 optimal weight: 0.3980 chunk 13 optimal weight: 2.9990 chunk 14 optimal weight: 0.9980 chunk 15 optimal weight: 0.6980 chunk 10 optimal weight: 0.8980 chunk 16 optimal weight: 0.5980 chunk 9 optimal weight: 0.5980 chunk 7 optimal weight: 0.1980 chunk 1 optimal weight: 0.0870 chunk 8 optimal weight: 0.6980 overall best weight: 0.2758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 151 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7390 moved from start: 0.1792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 1481 Z= 0.212 Angle : 0.624 6.776 2029 Z= 0.311 Chirality : 0.049 0.218 264 Planarity : 0.005 0.035 258 Dihedral : 6.811 54.460 329 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.90 % Favored : 93.10 % Rotamer: Outliers : 1.25 % Allowed : 23.12 % Favored : 75.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.98 (0.64), residues: 174 helix: -2.86 (0.69), residues: 44 sheet: -2.81 (1.01), residues: 27 loop : -1.26 (0.65), residues: 103 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.004 TRP B 62 HIS 0.002 0.001 HIS B 64 PHE 0.010 0.002 PHE B 147 TYR 0.007 0.001 TYR B 103 ARG 0.001 0.000 ARG B 149 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 348 Ramachandran restraints generated. 174 Oldfield, 0 Emsley, 174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 348 Ramachandran restraints generated. 174 Oldfield, 0 Emsley, 174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 39 time to evaluate : 0.162 Fit side-chains revert: symmetry clash REVERT: B 41 ASN cc_start: 0.8161 (m110) cc_final: 0.7653 (t0) REVERT: B 161 MET cc_start: 0.5909 (mmp) cc_final: 0.5429 (mmp) outliers start: 2 outliers final: 1 residues processed: 40 average time/residue: 0.1065 time to fit residues: 5.0467 Evaluate side-chains 41 residues out of total 160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 40 time to evaluate : 0.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 145 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 17 random chunks: chunk 10 optimal weight: 0.4980 chunk 14 optimal weight: 0.0770 chunk 4 optimal weight: 0.9990 chunk 12 optimal weight: 0.5980 chunk 1 optimal weight: 0.8980 chunk 3 optimal weight: 0.9980 chunk 13 optimal weight: 0.5980 chunk 5 optimal weight: 0.5980 chunk 2 optimal weight: 0.8980 chunk 11 optimal weight: 0.5980 chunk 0 optimal weight: 0.1980 overall best weight: 0.3938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 151 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7401 moved from start: 0.1844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 1481 Z= 0.254 Angle : 0.629 6.251 2029 Z= 0.315 Chirality : 0.050 0.220 264 Planarity : 0.005 0.034 258 Dihedral : 6.792 54.187 329 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.20 % Favored : 90.80 % Rotamer: Outliers : 1.25 % Allowed : 23.75 % 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: -2.93 (0.64), residues: 174 helix: -2.86 (0.69), residues: 44 sheet: -2.76 (1.02), residues: 27 loop : -1.21 (0.65), residues: 103 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.005 TRP B 62 HIS 0.002 0.002 HIS B 64 PHE 0.011 0.002 PHE B 147 TYR 0.010 0.002 TYR B 103 ARG 0.001 0.000 ARG B 149 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 348 Ramachandran restraints generated. 174 Oldfield, 0 Emsley, 174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 348 Ramachandran restraints generated. 174 Oldfield, 0 Emsley, 174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 39 time to evaluate : 0.144 Fit side-chains revert: symmetry clash REVERT: B 41 ASN cc_start: 0.8179 (m110) cc_final: 0.7672 (t0) REVERT: B 161 MET cc_start: 0.5979 (mmp) cc_final: 0.5536 (mmp) outliers start: 2 outliers final: 1 residues processed: 40 average time/residue: 0.1109 time to fit residues: 5.1831 Evaluate side-chains 39 residues out of total 160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 38 time to evaluate : 0.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 145 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 17 random chunks: chunk 9 optimal weight: 0.9990 chunk 15 optimal weight: 0.0570 chunk 11 optimal weight: 0.5980 chunk 0 optimal weight: 0.9990 chunk 10 optimal weight: 0.6980 chunk 6 optimal weight: 0.6980 chunk 16 optimal weight: 0.3980 chunk 3 optimal weight: 0.0980 chunk 2 optimal weight: 0.0970 chunk 13 optimal weight: 0.8980 chunk 7 optimal weight: 0.5980 overall best weight: 0.2496 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 151 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7380 moved from start: 0.1819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 1481 Z= 0.202 Angle : 0.614 6.045 2029 Z= 0.308 Chirality : 0.048 0.213 264 Planarity : 0.005 0.034 258 Dihedral : 6.692 54.478 329 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 10.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.90 % Favored : 93.10 % Rotamer: Outliers : 1.25 % Allowed : 23.12 % Favored : 75.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.80 (0.65), residues: 174 helix: -2.64 (0.73), residues: 44 sheet: -3.07 (1.02), residues: 26 loop : -1.10 (0.65), residues: 104 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.005 TRP B 62 HIS 0.002 0.001 HIS B 64 PHE 0.008 0.001 PHE B 147 TYR 0.007 0.001 TYR B 103 ARG 0.001 0.000 ARG B 149 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 348 Ramachandran restraints generated. 174 Oldfield, 0 Emsley, 174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 348 Ramachandran restraints generated. 174 Oldfield, 0 Emsley, 174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 39 time to evaluate : 0.170 Fit side-chains revert: symmetry clash REVERT: B 40 THR cc_start: 0.8461 (m) cc_final: 0.8189 (t) REVERT: B 41 ASN cc_start: 0.8150 (m110) cc_final: 0.7614 (t0) REVERT: B 161 MET cc_start: 0.5956 (mmp) cc_final: 0.5525 (mmp) outliers start: 2 outliers final: 1 residues processed: 40 average time/residue: 0.1029 time to fit residues: 4.8371 Evaluate side-chains 40 residues out of total 160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 39 time to evaluate : 0.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 145 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 17 random chunks: chunk 1 optimal weight: 0.1980 chunk 4 optimal weight: 0.4980 chunk 3 optimal weight: 0.7980 chunk 10 optimal weight: 0.9990 chunk 5 optimal weight: 0.0010 chunk 8 optimal weight: 0.6980 chunk 0 optimal weight: 0.1980 chunk 16 optimal weight: 0.6980 chunk 6 optimal weight: 0.0980 chunk 12 optimal weight: 1.9990 chunk 14 optimal weight: 0.6980 overall best weight: 0.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 151 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.124404 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.103947 restraints weight = 2206.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.107700 restraints weight = 1205.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.110094 restraints weight = 790.933| |-----------------------------------------------------------------------------| r_work (final): 0.3398 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7366 moved from start: 0.1845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 1481 Z= 0.195 Angle : 0.599 5.772 2029 Z= 0.301 Chirality : 0.048 0.208 264 Planarity : 0.005 0.034 258 Dihedral : 6.489 54.188 329 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.32 % Favored : 93.68 % Rotamer: Outliers : 0.62 % Allowed : 22.50 % Favored : 76.88 % 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: -2.64 (0.66), residues: 174 helix: -2.53 (0.75), residues: 44 sheet: -3.01 (1.04), residues: 26 loop : -0.96 (0.66), residues: 104 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.005 TRP B 62 HIS 0.002 0.001 HIS B 64 PHE 0.007 0.001 PHE B 147 TYR 0.006 0.001 TYR B 103 ARG 0.001 0.000 ARG B 130 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1077.49 seconds wall clock time: 19 minutes 39.19 seconds (1179.19 seconds total)