Starting phenix.real_space_refine on Thu Nov 14 05:08:59 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hfc_34717/11_2024/8hfc_34717.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hfc_34717/11_2024/8hfc_34717.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hfc_34717/11_2024/8hfc_34717.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hfc_34717/11_2024/8hfc_34717.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hfc_34717/11_2024/8hfc_34717.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hfc_34717/11_2024/8hfc_34717.cif" } resolution = 3.5 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= 0.004 sd= 0.145 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 Zn 2 6.06 5 S 22 5.16 5 C 2590 2.51 5 N 694 2.21 5 O 699 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 4007 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 2234 Number of conformers: 1 Conformer: "" Number of residues, atoms: 276, 2234 Classifications: {'peptide': 276} Link IDs: {'PTRANS': 16, 'TRANS': 259} Chain: "B" Number of atoms: 1756 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1756 Classifications: {'peptide': 222} Link IDs: {'PTRANS': 13, 'TRANS': 208} Chain: "A" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 17 Unusual residues: {' ZN': 2, 'PLM': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'PLM:plan-1': 1} Unresolved non-hydrogen planarities: 1 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 953 SG CYS A 189 39.293 32.069 58.239 1.00 43.49 S ATOM 972 SG CYS A 192 39.223 35.988 57.314 1.00 49.55 S ATOM 1110 SG CYS A 209 36.468 33.802 57.411 1.00 32.51 S ATOM 837 SG CYS A 175 39.498 31.365 69.663 1.00 35.51 S ATOM 856 SG CYS A 178 38.830 35.231 68.292 1.00 36.69 S ATOM 993 SG CYS A 195 36.831 32.303 67.459 1.00 31.03 S Time building chain proxies: 3.00, per 1000 atoms: 0.75 Number of scatterers: 4007 At special positions: 0 Unit cell: (60.872, 65.22, 117.396, 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) Zn 2 29.99 S 22 16.00 O 699 8.00 N 694 7.00 C 2590 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS B 114 " - pdb=" SG CYS B 126 " 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.12 Conformation dependent library (CDL) restraints added in 624.4 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 402 " pdb="ZN ZN A 402 " - pdb=" ND1 HIS A 202 " pdb="ZN ZN A 402 " - pdb=" SG CYS A 209 " pdb="ZN ZN A 402 " - pdb=" SG CYS A 189 " pdb="ZN ZN A 402 " - pdb=" SG CYS A 192 " pdb=" ZN A 403 " pdb="ZN ZN A 403 " - pdb=" ND1 HIS A 188 " pdb="ZN ZN A 403 " - pdb=" SG CYS A 175 " pdb="ZN ZN A 403 " - pdb=" SG CYS A 178 " pdb="ZN ZN A 403 " - pdb=" SG CYS A 195 " Number of angles added : 6 988 Ramachandran restraints generated. 494 Oldfield, 0 Emsley, 494 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 928 Finding SS restraints... Secondary structure from input PDB file: 16 helices and 7 sheets defined 41.2% alpha, 5.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.40 Creating SS restraints... Processing helix chain 'A' and resid 76 through 94 removed outlier: 3.807A pdb=" N VAL A 80 " --> pdb=" O LEU A 76 " (cutoff:3.500A) Proline residue: A 87 - end of helix removed outlier: 3.874A pdb=" N PHE A 94 " --> pdb=" O LEU A 90 " (cutoff:3.500A) Processing helix chain 'A' and resid 106 through 129 Processing helix chain 'A' and resid 214 through 243 Processing helix chain 'A' and resid 246 through 249 Processing helix chain 'A' and resid 250 through 264 removed outlier: 4.000A pdb=" N ILE A 254 " --> pdb=" O CYS A 250 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 279 removed outlier: 3.606A pdb=" N ALA A 268 " --> pdb=" O LEU A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 283 through 291 Processing helix chain 'A' and resid 313 through 323 Processing helix chain 'B' and resid 45 through 49 Processing helix chain 'B' and resid 65 through 69 Processing helix chain 'B' and resid 130 through 135 Processing helix chain 'B' and resid 137 through 157 Processing helix chain 'B' and resid 161 through 174 Processing helix chain 'B' and resid 188 through 190 No H-bonds generated for 'chain 'B' and resid 188 through 190' Processing helix chain 'B' and resid 191 through 206 removed outlier: 3.864A pdb=" N LEU B 195 " --> pdb=" O PHE B 191 " (cutoff:3.500A) Processing helix chain 'B' and resid 209 through 215 removed outlier: 3.643A pdb=" N ARG B 214 " --> pdb=" O LEU B 210 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 158 through 160 Processing sheet with id=AA2, first strand: chain 'A' and resid 174 through 175 removed outlier: 3.825A pdb=" N ILE A 180 " --> pdb=" O CYS A 175 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 187 through 189 removed outlier: 3.774A pdb=" N VAL A 194 " --> pdb=" O CYS A 189 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 202 through 203 Processing sheet with id=AA5, first strand: chain 'B' and resid 27 through 28 Processing sheet with id=AA6, first strand: chain 'B' and resid 32 through 33 Processing sheet with id=AA7, first strand: chain 'B' and resid 70 through 75 160 hydrogen bonds defined for protein. 435 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: 1.00 Time building geometry restraints manager: 1.07 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1281 1.34 - 1.46: 843 1.46 - 1.58: 1967 1.58 - 1.70: 1 1.70 - 1.82: 29 Bond restraints: 4121 Sorted by residual: bond pdb=" C1 PLM A 401 " pdb=" C2 PLM A 401 " ideal model delta sigma weight residual 1.542 1.599 -0.057 2.00e-02 2.50e+03 8.25e+00 bond pdb=" CA VAL B 233 " pdb=" CB VAL B 233 " ideal model delta sigma weight residual 1.546 1.534 0.012 8.80e-03 1.29e+04 1.95e+00 bond pdb=" C6 PLM A 401 " pdb=" C7 PLM A 401 " ideal model delta sigma weight residual 1.525 1.552 -0.027 2.00e-02 2.50e+03 1.87e+00 bond pdb=" C2 PLM A 401 " pdb=" C3 PLM A 401 " ideal model delta sigma weight residual 1.522 1.549 -0.027 2.00e-02 2.50e+03 1.84e+00 bond pdb=" CB TRP A 117 " pdb=" CG TRP A 117 " ideal model delta sigma weight residual 1.498 1.456 0.042 3.10e-02 1.04e+03 1.84e+00 ... (remaining 4116 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.41: 5343 1.41 - 2.82: 207 2.82 - 4.23: 36 4.23 - 5.64: 4 5.64 - 7.05: 5 Bond angle restraints: 5595 Sorted by residual: angle pdb=" C TYR B 117 " pdb=" N ASP B 118 " pdb=" CA ASP B 118 " ideal model delta sigma weight residual 121.54 128.59 -7.05 1.91e+00 2.74e-01 1.36e+01 angle pdb=" N ILE A 93 " pdb=" CA ILE A 93 " pdb=" C ILE A 93 " ideal model delta sigma weight residual 111.81 108.81 3.00 8.60e-01 1.35e+00 1.22e+01 angle pdb=" C ARG B 116 " pdb=" N TYR B 117 " pdb=" CA TYR B 117 " ideal model delta sigma weight residual 121.54 127.66 -6.12 1.91e+00 2.74e-01 1.03e+01 angle pdb=" C ASP A 341 " pdb=" N TRP A 342 " pdb=" CA TRP A 342 " ideal model delta sigma weight residual 121.54 125.75 -4.21 1.91e+00 2.74e-01 4.86e+00 angle pdb=" N ARG B 188 " pdb=" CA ARG B 188 " pdb=" C ARG B 188 " ideal model delta sigma weight residual 109.81 114.56 -4.75 2.21e+00 2.05e-01 4.61e+00 ... (remaining 5590 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.51: 2036 17.51 - 35.01: 288 35.01 - 52.52: 78 52.52 - 70.03: 16 70.03 - 87.53: 7 Dihedral angle restraints: 2425 sinusoidal: 982 harmonic: 1443 Sorted by residual: dihedral pdb=" CA ARG B 188 " pdb=" C ARG B 188 " pdb=" N PRO B 189 " pdb=" CA PRO B 189 " ideal model delta harmonic sigma weight residual -180.00 -160.89 -19.11 0 5.00e+00 4.00e-02 1.46e+01 dihedral pdb=" CA GLY B 176 " pdb=" C GLY B 176 " pdb=" N LEU B 177 " pdb=" CA LEU B 177 " ideal model delta harmonic sigma weight residual -180.00 -160.92 -19.08 0 5.00e+00 4.00e-02 1.46e+01 dihedral pdb=" CA LEU B 185 " pdb=" C LEU B 185 " pdb=" N LEU B 186 " pdb=" CA LEU B 186 " ideal model delta harmonic sigma weight residual -180.00 -161.50 -18.50 0 5.00e+00 4.00e-02 1.37e+01 ... (remaining 2422 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 275 0.027 - 0.053: 184 0.053 - 0.079: 92 0.079 - 0.106: 43 0.106 - 0.132: 12 Chirality restraints: 606 Sorted by residual: chirality pdb=" CA VAL B 233 " pdb=" N VAL B 233 " pdb=" C VAL B 233 " pdb=" CB VAL B 233 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.39e-01 chirality pdb=" CA VAL B 216 " pdb=" N VAL B 216 " pdb=" C VAL B 216 " pdb=" CB VAL B 216 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.07e-01 chirality pdb=" CA PRO A 267 " pdb=" N PRO A 267 " pdb=" C PRO A 267 " pdb=" CB PRO A 267 " both_signs ideal model delta sigma weight residual False 2.72 2.59 0.13 2.00e-01 2.50e+01 4.01e-01 ... (remaining 603 not shown) Planarity restraints: 713 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR A 266 " 0.032 5.00e-02 4.00e+02 4.78e-02 3.65e+00 pdb=" N PRO A 267 " -0.083 5.00e-02 4.00e+02 pdb=" CA PRO A 267 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 267 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR B 88 " 0.023 5.00e-02 4.00e+02 3.53e-02 2.00e+00 pdb=" N PRO B 89 " -0.061 5.00e-02 4.00e+02 pdb=" CA PRO B 89 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO B 89 " 0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE B 55 " 0.019 5.00e-02 4.00e+02 2.85e-02 1.30e+00 pdb=" N PRO B 56 " -0.049 5.00e-02 4.00e+02 pdb=" CA PRO B 56 " 0.014 5.00e-02 4.00e+02 pdb=" CD PRO B 56 " 0.016 5.00e-02 4.00e+02 ... (remaining 710 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 186 2.71 - 3.26: 3917 3.26 - 3.81: 6278 3.81 - 4.35: 7274 4.35 - 4.90: 13142 Nonbonded interactions: 30797 Sorted by model distance: nonbonded pdb=" O SER B 224 " pdb=" OG SER B 224 " model vdw 2.164 3.040 nonbonded pdb=" OH TYR B 59 " pdb=" OD2 ASP B 230 " model vdw 2.203 3.040 nonbonded pdb=" O TYR B 135 " pdb=" NH1 ARG B 214 " model vdw 2.203 3.120 nonbonded pdb=" O ALA A 83 " pdb=" OH TYR A 259 " model vdw 2.211 3.040 nonbonded pdb=" OE2 GLU B 155 " pdb=" OG SER B 194 " model vdw 2.238 3.040 ... (remaining 30792 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: 0.410 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: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 14.430 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 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 : 0.007 0.069 4121 Z= 0.451 Angle : 0.671 7.046 5595 Z= 0.372 Chirality : 0.046 0.132 606 Planarity : 0.004 0.048 713 Dihedral : 18.011 87.532 1494 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.20 % Allowed : 6.48 % Favored : 93.32 % Rotamer: Outliers : 3.88 % Allowed : 24.20 % Favored : 71.92 % 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: -2.90 (0.33), residues: 494 helix: -0.85 (0.34), residues: 175 sheet: -2.79 (0.61), residues: 40 loop : -2.60 (0.34), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 162 HIS 0.003 0.001 HIS A 202 PHE 0.013 0.002 PHE A 218 TYR 0.011 0.002 TYR B 117 ARG 0.003 0.000 ARG B 83 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 988 Ramachandran restraints generated. 494 Oldfield, 0 Emsley, 494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 988 Ramachandran restraints generated. 494 Oldfield, 0 Emsley, 494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 68 time to evaluate : 0.462 Fit side-chains REVERT: A 153 GLU cc_start: 0.8224 (mp0) cc_final: 0.7935 (mp0) REVERT: B 116 ARG cc_start: 0.7613 (mtm-85) cc_final: 0.7324 (mmm-85) REVERT: B 222 ARG cc_start: 0.8421 (tmt170) cc_final: 0.8093 (tmt170) outliers start: 17 outliers final: 12 residues processed: 82 average time/residue: 0.1669 time to fit residues: 16.9533 Evaluate side-chains 70 residues out of total 438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 58 time to evaluate : 0.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 86 CYS Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 123 SER Chi-restraints excluded: chain A residue 166 ILE Chi-restraints excluded: chain A residue 192 CYS Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain B residue 126 CYS Chi-restraints excluded: chain B residue 166 SER Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain B residue 232 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 41 optimal weight: 0.0770 chunk 37 optimal weight: 9.9990 chunk 20 optimal weight: 0.7980 chunk 12 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 chunk 19 optimal weight: 0.8980 chunk 38 optimal weight: 0.0270 chunk 14 optimal weight: 0.5980 chunk 23 optimal weight: 0.0670 chunk 28 optimal weight: 0.6980 chunk 44 optimal weight: 3.9990 overall best weight: 0.2934 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 199 HIS A 282 GLN A 296 ASN A 300 HIS A 307 ASN A 320 HIS ** B 24 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 149 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7828 moved from start: 0.1364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 4121 Z= 0.128 Angle : 0.524 6.755 5595 Z= 0.274 Chirality : 0.041 0.135 606 Planarity : 0.004 0.031 713 Dihedral : 6.678 56.598 575 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 4.11 % Allowed : 23.97 % Favored : 71.92 % 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: -1.17 (0.37), residues: 494 helix: 0.72 (0.37), residues: 190 sheet: -1.28 (0.78), residues: 34 loop : -1.90 (0.37), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 178 HIS 0.005 0.001 HIS B 212 PHE 0.008 0.001 PHE B 231 TYR 0.017 0.001 TYR B 200 ARG 0.003 0.000 ARG A 242 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 988 Ramachandran restraints generated. 494 Oldfield, 0 Emsley, 494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 988 Ramachandran restraints generated. 494 Oldfield, 0 Emsley, 494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 76 time to evaluate : 0.444 Fit side-chains REVERT: A 88 MET cc_start: 0.7364 (tmm) cc_final: 0.7154 (tmm) REVERT: A 147 ASN cc_start: 0.9173 (t0) cc_final: 0.8587 (t0) REVERT: A 153 GLU cc_start: 0.8218 (mp0) cc_final: 0.7769 (mp0) REVERT: A 239 HIS cc_start: 0.8333 (t-170) cc_final: 0.7890 (t-170) REVERT: A 291 ILE cc_start: 0.6114 (OUTLIER) cc_final: 0.5777 (tt) REVERT: B 214 ARG cc_start: 0.7311 (mmt90) cc_final: 0.6700 (mmm-85) REVERT: B 222 ARG cc_start: 0.8439 (tmt170) cc_final: 0.8192 (tmt170) outliers start: 18 outliers final: 7 residues processed: 88 average time/residue: 0.1762 time to fit residues: 19.5527 Evaluate side-chains 72 residues out of total 438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 64 time to evaluate : 0.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 172 ILE Chi-restraints excluded: chain A residue 243 GLU Chi-restraints excluded: chain A residue 273 TYR Chi-restraints excluded: chain A residue 291 ILE Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain B residue 25 GLU Chi-restraints excluded: chain B residue 104 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 24 optimal weight: 0.9980 chunk 13 optimal weight: 2.9990 chunk 37 optimal weight: 0.5980 chunk 30 optimal weight: 0.9990 chunk 12 optimal weight: 0.9990 chunk 44 optimal weight: 0.9980 chunk 48 optimal weight: 2.9990 chunk 39 optimal weight: 0.9990 chunk 15 optimal weight: 1.9990 chunk 35 optimal weight: 0.0980 chunk 33 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 24 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 68 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 moved from start: 0.1695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 4121 Z= 0.171 Angle : 0.528 7.494 5595 Z= 0.267 Chirality : 0.041 0.135 606 Planarity : 0.004 0.033 713 Dihedral : 5.003 38.080 561 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 5.25 % Allowed : 24.20 % Favored : 70.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.59 (0.38), residues: 494 helix: 1.37 (0.39), residues: 190 sheet: -1.25 (0.68), residues: 44 loop : -1.66 (0.38), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 178 HIS 0.003 0.001 HIS B 212 PHE 0.009 0.001 PHE B 231 TYR 0.012 0.001 TYR B 200 ARG 0.003 0.000 ARG B 116 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 988 Ramachandran restraints generated. 494 Oldfield, 0 Emsley, 494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 988 Ramachandran restraints generated. 494 Oldfield, 0 Emsley, 494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 70 time to evaluate : 0.470 Fit side-chains REVERT: A 88 MET cc_start: 0.7312 (tmm) cc_final: 0.7084 (tmm) REVERT: A 153 GLU cc_start: 0.8197 (mp0) cc_final: 0.7809 (mp0) REVERT: A 239 HIS cc_start: 0.8499 (t-170) cc_final: 0.8287 (t-170) REVERT: B 94 GLN cc_start: 0.8709 (mt0) cc_final: 0.8464 (tt0) REVERT: B 116 ARG cc_start: 0.7930 (mmm-85) cc_final: 0.7648 (mmm-85) REVERT: B 205 ASN cc_start: 0.7682 (m-40) cc_final: 0.7448 (m-40) outliers start: 23 outliers final: 13 residues processed: 87 average time/residue: 0.1783 time to fit residues: 19.1297 Evaluate side-chains 77 residues out of total 438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 64 time to evaluate : 0.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 166 ILE Chi-restraints excluded: chain A residue 172 ILE Chi-restraints excluded: chain A residue 243 GLU Chi-restraints excluded: chain A residue 318 MET Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain B residue 25 GLU Chi-restraints excluded: chain B residue 104 VAL Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 232 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 23 optimal weight: 2.9990 chunk 4 optimal weight: 0.5980 chunk 21 optimal weight: 0.9980 chunk 29 optimal weight: 0.0060 chunk 44 optimal weight: 0.5980 chunk 47 optimal weight: 0.9980 chunk 42 optimal weight: 0.9990 chunk 12 optimal weight: 1.9990 chunk 39 optimal weight: 0.3980 chunk 26 optimal weight: 8.9990 chunk 0 optimal weight: 2.9990 overall best weight: 0.5196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 24 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7817 moved from start: 0.2046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 4121 Z= 0.149 Angle : 0.497 6.123 5595 Z= 0.255 Chirality : 0.040 0.128 606 Planarity : 0.004 0.034 713 Dihedral : 4.682 33.857 561 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 3.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 4.11 % Allowed : 24.89 % Favored : 71.00 % 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: -0.10 (0.38), residues: 494 helix: 1.81 (0.39), residues: 184 sheet: -0.55 (0.78), residues: 34 loop : -1.40 (0.37), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 178 HIS 0.005 0.001 HIS B 212 PHE 0.009 0.001 PHE A 287 TYR 0.011 0.001 TYR A 115 ARG 0.002 0.000 ARG B 116 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 988 Ramachandran restraints generated. 494 Oldfield, 0 Emsley, 494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 988 Ramachandran restraints generated. 494 Oldfield, 0 Emsley, 494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 72 time to evaluate : 0.481 Fit side-chains REVERT: A 88 MET cc_start: 0.7229 (tmm) cc_final: 0.6996 (tmm) REVERT: A 153 GLU cc_start: 0.8202 (mp0) cc_final: 0.7787 (mp0) REVERT: A 291 ILE cc_start: 0.6126 (OUTLIER) cc_final: 0.5851 (tt) REVERT: A 321 LEU cc_start: 0.8949 (OUTLIER) cc_final: 0.8728 (tm) REVERT: B 205 ASN cc_start: 0.7819 (m-40) cc_final: 0.7527 (m-40) outliers start: 18 outliers final: 12 residues processed: 84 average time/residue: 0.1474 time to fit residues: 15.8298 Evaluate side-chains 77 residues out of total 438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 63 time to evaluate : 0.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 125 ILE Chi-restraints excluded: chain A residue 166 ILE Chi-restraints excluded: chain A residue 172 ILE Chi-restraints excluded: chain A residue 291 ILE Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain B residue 25 GLU Chi-restraints excluded: chain B residue 30 PHE Chi-restraints excluded: chain B residue 104 VAL Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain B residue 232 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 35 optimal weight: 0.8980 chunk 19 optimal weight: 0.9990 chunk 40 optimal weight: 1.9990 chunk 32 optimal weight: 0.7980 chunk 0 optimal weight: 2.9990 chunk 24 optimal weight: 3.9990 chunk 42 optimal weight: 0.9980 chunk 11 optimal weight: 5.9990 chunk 15 optimal weight: 0.5980 chunk 9 optimal weight: 2.9990 chunk 27 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 24 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 moved from start: 0.2071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 4121 Z= 0.201 Angle : 0.545 8.792 5595 Z= 0.267 Chirality : 0.041 0.134 606 Planarity : 0.004 0.034 713 Dihedral : 4.741 33.684 561 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 3.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 4.34 % Allowed : 24.43 % Favored : 71.23 % 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: -0.10 (0.38), residues: 494 helix: 1.91 (0.39), residues: 184 sheet: -1.04 (0.66), residues: 44 loop : -1.39 (0.38), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 178 HIS 0.010 0.001 HIS A 239 PHE 0.011 0.001 PHE B 231 TYR 0.010 0.001 TYR A 115 ARG 0.002 0.000 ARG A 242 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 988 Ramachandran restraints generated. 494 Oldfield, 0 Emsley, 494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 988 Ramachandran restraints generated. 494 Oldfield, 0 Emsley, 494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 66 time to evaluate : 0.433 Fit side-chains REVERT: A 88 MET cc_start: 0.7365 (tmm) cc_final: 0.7120 (tmm) REVERT: A 153 GLU cc_start: 0.8187 (mp0) cc_final: 0.7807 (mp0) REVERT: A 291 ILE cc_start: 0.6183 (OUTLIER) cc_final: 0.5911 (tt) REVERT: B 116 ARG cc_start: 0.8234 (mmm-85) cc_final: 0.7922 (mmm-85) REVERT: B 205 ASN cc_start: 0.7881 (m-40) cc_final: 0.7528 (m-40) outliers start: 19 outliers final: 14 residues processed: 80 average time/residue: 0.1535 time to fit residues: 15.7022 Evaluate side-chains 81 residues out of total 438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 66 time to evaluate : 0.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 130 SER Chi-restraints excluded: chain A residue 166 ILE Chi-restraints excluded: chain A residue 172 ILE Chi-restraints excluded: chain A residue 258 CYS Chi-restraints excluded: chain A residue 291 ILE Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain B residue 25 GLU Chi-restraints excluded: chain B residue 30 PHE Chi-restraints excluded: chain B residue 104 VAL Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain B residue 232 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 11 optimal weight: 2.9990 chunk 47 optimal weight: 3.9990 chunk 39 optimal weight: 0.9980 chunk 21 optimal weight: 0.0670 chunk 3 optimal weight: 2.9990 chunk 15 optimal weight: 0.9990 chunk 24 optimal weight: 3.9990 chunk 45 optimal weight: 1.9990 chunk 5 optimal weight: 0.8980 chunk 27 optimal weight: 4.9990 chunk 34 optimal weight: 0.0970 overall best weight: 0.6118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 24 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7824 moved from start: 0.2249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 4121 Z= 0.164 Angle : 0.525 8.439 5595 Z= 0.262 Chirality : 0.041 0.135 606 Planarity : 0.004 0.034 713 Dihedral : 4.648 33.871 561 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 3.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 4.79 % Allowed : 24.89 % Favored : 70.32 % 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: 0.14 (0.38), residues: 494 helix: 2.03 (0.38), residues: 184 sheet: -0.50 (0.77), residues: 34 loop : -1.26 (0.38), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 178 HIS 0.009 0.001 HIS A 239 PHE 0.010 0.001 PHE B 231 TYR 0.013 0.001 TYR B 200 ARG 0.001 0.000 ARG B 214 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 988 Ramachandran restraints generated. 494 Oldfield, 0 Emsley, 494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 988 Ramachandran restraints generated. 494 Oldfield, 0 Emsley, 494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 68 time to evaluate : 0.471 Fit side-chains REVERT: A 88 MET cc_start: 0.7264 (tmm) cc_final: 0.7015 (tmm) REVERT: A 153 GLU cc_start: 0.8176 (mp0) cc_final: 0.7813 (mp0) REVERT: A 291 ILE cc_start: 0.6147 (OUTLIER) cc_final: 0.5892 (tt) REVERT: B 205 ASN cc_start: 0.7997 (m-40) cc_final: 0.7636 (m-40) outliers start: 21 outliers final: 14 residues processed: 84 average time/residue: 0.1371 time to fit residues: 15.1915 Evaluate side-chains 79 residues out of total 438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 64 time to evaluate : 0.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 125 ILE Chi-restraints excluded: chain A residue 130 SER Chi-restraints excluded: chain A residue 166 ILE Chi-restraints excluded: chain A residue 172 ILE Chi-restraints excluded: chain A residue 291 ILE Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain B residue 25 GLU Chi-restraints excluded: chain B residue 30 PHE Chi-restraints excluded: chain B residue 104 VAL Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain B residue 232 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 26 optimal weight: 2.9990 chunk 39 optimal weight: 0.9980 chunk 47 optimal weight: 0.7980 chunk 29 optimal weight: 0.5980 chunk 28 optimal weight: 0.9990 chunk 21 optimal weight: 1.9990 chunk 18 optimal weight: 0.9980 chunk 14 optimal weight: 1.9990 chunk 9 optimal weight: 2.9990 chunk 30 optimal weight: 3.9990 chunk 32 optimal weight: 1.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 24 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 moved from start: 0.2280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4121 Z= 0.203 Angle : 0.556 8.467 5595 Z= 0.273 Chirality : 0.041 0.139 606 Planarity : 0.004 0.034 713 Dihedral : 4.666 33.516 561 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 3.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 4.11 % Allowed : 25.57 % Favored : 70.32 % 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: 0.17 (0.38), residues: 494 helix: 2.04 (0.38), residues: 184 sheet: -0.43 (0.78), residues: 34 loop : -1.23 (0.38), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 178 HIS 0.010 0.001 HIS A 239 PHE 0.010 0.001 PHE B 231 TYR 0.010 0.001 TYR A 115 ARG 0.001 0.000 ARG B 116 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 988 Ramachandran restraints generated. 494 Oldfield, 0 Emsley, 494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 988 Ramachandran restraints generated. 494 Oldfield, 0 Emsley, 494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 66 time to evaluate : 0.458 Fit side-chains REVERT: A 88 MET cc_start: 0.7346 (tmm) cc_final: 0.7106 (tmm) REVERT: A 153 GLU cc_start: 0.8181 (mp0) cc_final: 0.7818 (mp0) REVERT: A 291 ILE cc_start: 0.6163 (OUTLIER) cc_final: 0.5959 (tt) REVERT: B 69 VAL cc_start: 0.8983 (t) cc_final: 0.8770 (p) REVERT: B 205 ASN cc_start: 0.8073 (m-40) cc_final: 0.7695 (m-40) outliers start: 18 outliers final: 16 residues processed: 80 average time/residue: 0.1270 time to fit residues: 13.6074 Evaluate side-chains 81 residues out of total 438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 64 time to evaluate : 0.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 130 SER Chi-restraints excluded: chain A residue 166 ILE Chi-restraints excluded: chain A residue 172 ILE Chi-restraints excluded: chain A residue 258 CYS Chi-restraints excluded: chain A residue 291 ILE Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain B residue 25 GLU Chi-restraints excluded: chain B residue 30 PHE Chi-restraints excluded: chain B residue 104 VAL Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 156 GLU Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain B residue 232 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 23 optimal weight: 2.9990 chunk 4 optimal weight: 0.6980 chunk 37 optimal weight: 8.9990 chunk 42 optimal weight: 0.8980 chunk 45 optimal weight: 5.9990 chunk 41 optimal weight: 0.8980 chunk 44 optimal weight: 6.9990 chunk 26 optimal weight: 3.9990 chunk 19 optimal weight: 0.6980 chunk 34 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 24 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7862 moved from start: 0.2309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 4121 Z= 0.230 Angle : 0.551 8.499 5595 Z= 0.275 Chirality : 0.042 0.133 606 Planarity : 0.004 0.034 713 Dihedral : 4.739 33.916 561 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 3.88 % Allowed : 26.26 % Favored : 69.86 % 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: 0.06 (0.38), residues: 494 helix: 1.80 (0.38), residues: 190 sheet: -0.72 (0.78), residues: 32 loop : -1.20 (0.38), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 178 HIS 0.011 0.001 HIS A 239 PHE 0.010 0.001 PHE B 231 TYR 0.017 0.001 TYR B 200 ARG 0.002 0.000 ARG A 126 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 988 Ramachandran restraints generated. 494 Oldfield, 0 Emsley, 494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 988 Ramachandran restraints generated. 494 Oldfield, 0 Emsley, 494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 70 time to evaluate : 0.477 Fit side-chains REVERT: A 88 MET cc_start: 0.7368 (tmm) cc_final: 0.7127 (tmm) REVERT: A 153 GLU cc_start: 0.8150 (mp0) cc_final: 0.7797 (mp0) REVERT: A 291 ILE cc_start: 0.6207 (OUTLIER) cc_final: 0.5992 (tt) REVERT: B 205 ASN cc_start: 0.8092 (m-40) cc_final: 0.7751 (m-40) outliers start: 17 outliers final: 14 residues processed: 83 average time/residue: 0.1402 time to fit residues: 15.1045 Evaluate side-chains 81 residues out of total 438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 66 time to evaluate : 0.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 130 SER Chi-restraints excluded: chain A residue 166 ILE Chi-restraints excluded: chain A residue 291 ILE Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain B residue 25 GLU Chi-restraints excluded: chain B residue 30 PHE Chi-restraints excluded: chain B residue 104 VAL Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 156 GLU Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain B residue 232 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 39 optimal weight: 2.9990 chunk 41 optimal weight: 0.0170 chunk 43 optimal weight: 2.9990 chunk 28 optimal weight: 4.9990 chunk 46 optimal weight: 1.9990 chunk 22 optimal weight: 6.9990 chunk 32 optimal weight: 0.9980 chunk 48 optimal weight: 0.9990 chunk 44 optimal weight: 0.6980 chunk 38 optimal weight: 0.0970 chunk 4 optimal weight: 0.5980 overall best weight: 0.4816 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 24 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7813 moved from start: 0.2583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 4121 Z= 0.152 Angle : 0.563 8.730 5595 Z= 0.271 Chirality : 0.041 0.149 606 Planarity : 0.004 0.034 713 Dihedral : 4.508 33.155 561 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 2.74 % Allowed : 27.17 % Favored : 70.09 % 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: 0.28 (0.39), residues: 494 helix: 2.01 (0.38), residues: 190 sheet: -0.65 (0.79), residues: 32 loop : -1.10 (0.38), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 100 HIS 0.011 0.001 HIS A 239 PHE 0.010 0.001 PHE B 231 TYR 0.010 0.001 TYR A 115 ARG 0.006 0.000 ARG B 116 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 988 Ramachandran restraints generated. 494 Oldfield, 0 Emsley, 494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 988 Ramachandran restraints generated. 494 Oldfield, 0 Emsley, 494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 67 time to evaluate : 0.478 Fit side-chains REVERT: A 88 MET cc_start: 0.7285 (tmm) cc_final: 0.7054 (tmm) REVERT: A 153 GLU cc_start: 0.8119 (mp0) cc_final: 0.7764 (mp0) REVERT: B 205 ASN cc_start: 0.8059 (m-40) cc_final: 0.7722 (m-40) outliers start: 12 outliers final: 12 residues processed: 76 average time/residue: 0.1418 time to fit residues: 13.9812 Evaluate side-chains 77 residues out of total 438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 65 time to evaluate : 0.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 130 SER Chi-restraints excluded: chain A residue 172 ILE Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain B residue 25 GLU Chi-restraints excluded: chain B residue 30 PHE Chi-restraints excluded: chain B residue 104 VAL Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain B residue 232 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 30 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 41 optimal weight: 0.0970 chunk 11 optimal weight: 0.9980 chunk 35 optimal weight: 0.0670 chunk 5 optimal weight: 0.0370 chunk 10 optimal weight: 0.0470 chunk 38 optimal weight: 1.9990 chunk 16 optimal weight: 0.9980 chunk 39 optimal weight: 3.9990 chunk 4 optimal weight: 0.5980 overall best weight: 0.1692 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 HIS ** B 24 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7768 moved from start: 0.2886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 4121 Z= 0.139 Angle : 0.542 8.330 5595 Z= 0.269 Chirality : 0.040 0.139 606 Planarity : 0.004 0.035 713 Dihedral : 4.321 30.946 561 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 2.74 % Allowed : 27.63 % Favored : 69.63 % 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: 0.43 (0.39), residues: 494 helix: 2.18 (0.38), residues: 190 sheet: -0.48 (0.80), residues: 32 loop : -1.06 (0.38), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 100 HIS 0.012 0.001 HIS A 239 PHE 0.010 0.001 PHE A 287 TYR 0.019 0.001 TYR B 200 ARG 0.009 0.000 ARG B 116 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 988 Ramachandran restraints generated. 494 Oldfield, 0 Emsley, 494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 988 Ramachandran restraints generated. 494 Oldfield, 0 Emsley, 494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 67 time to evaluate : 0.467 Fit side-chains REVERT: A 88 MET cc_start: 0.7436 (tmm) cc_final: 0.7177 (tmm) REVERT: A 153 GLU cc_start: 0.8109 (mp0) cc_final: 0.7739 (mp0) REVERT: B 116 ARG cc_start: 0.7882 (tpp80) cc_final: 0.7421 (ttm-80) REVERT: B 165 LEU cc_start: 0.8389 (mt) cc_final: 0.7980 (mt) REVERT: B 205 ASN cc_start: 0.7855 (m-40) cc_final: 0.7646 (m-40) outliers start: 12 outliers final: 11 residues processed: 74 average time/residue: 0.1567 time to fit residues: 14.8710 Evaluate side-chains 76 residues out of total 438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 65 time to evaluate : 0.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 130 SER Chi-restraints excluded: chain A residue 172 ILE Chi-restraints excluded: chain A residue 239 HIS Chi-restraints excluded: chain B residue 25 GLU Chi-restraints excluded: chain B residue 30 PHE Chi-restraints excluded: chain B residue 104 VAL Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain B residue 232 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 7 optimal weight: 0.9990 chunk 34 optimal weight: 0.7980 chunk 2 optimal weight: 0.8980 chunk 28 optimal weight: 3.9990 chunk 44 optimal weight: 1.9990 chunk 26 optimal weight: 0.9980 chunk 33 optimal weight: 0.5980 chunk 1 optimal weight: 0.5980 chunk 31 optimal weight: 0.0470 chunk 29 optimal weight: 8.9990 chunk 19 optimal weight: 1.9990 overall best weight: 0.5878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 24 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.177947 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.131163 restraints weight = 4630.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.133685 restraints weight = 4354.703| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.136248 restraints weight = 2959.153| |-----------------------------------------------------------------------------| r_work (final): 0.3213 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7661 moved from start: 0.2833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4121 Z= 0.175 Angle : 0.580 9.307 5595 Z= 0.277 Chirality : 0.041 0.135 606 Planarity : 0.004 0.035 713 Dihedral : 4.074 20.097 559 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 2.28 % Allowed : 27.85 % Favored : 69.86 % 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: 0.49 (0.39), residues: 494 helix: 2.28 (0.38), residues: 190 sheet: -0.50 (0.81), residues: 32 loop : -1.06 (0.38), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 178 HIS 0.016 0.001 HIS A 239 PHE 0.010 0.001 PHE A 287 TYR 0.010 0.001 TYR A 115 ARG 0.007 0.000 ARG B 116 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1226.03 seconds wall clock time: 22 minutes 51.21 seconds (1371.21 seconds total)