Starting phenix.real_space_refine on Wed Mar 5 23:43:44 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hfc_34717/03_2025/8hfc_34717.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hfc_34717/03_2025/8hfc_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/cci-nas-00/data/ceres_data/8hfc_34717/03_2025/8hfc_34717.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hfc_34717/03_2025/8hfc_34717.map" model { file = "/net/cci-nas-00/data/ceres_data/8hfc_34717/03_2025/8hfc_34717.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hfc_34717/03_2025/8hfc_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-5624/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: 2.63, per 1000 atoms: 0.66 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: 0.91 Conformation dependent library (CDL) restraints added in 407.5 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: 0.41 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: 1.02 Time building geometry restraints manager: 1.04 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: 0.610 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: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 13.880 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:4.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.850 ------------------------------------------------------------------------------- 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 : 0.466 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: 0.1742 time to fit residues: 17.6781 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 : 0.423 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.172392 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.121715 restraints weight = 4532.586| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.125304 restraints weight = 3144.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.127523 restraints weight = 2556.010| |-----------------------------------------------------------------------------| r_work (final): 0.3129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7622 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 56.600 575 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 : 0.455 Fit side-chains REVERT: A 88 MET cc_start: 0.7403 (tmm) cc_final: 0.7155 (tmm) REVERT: A 147 ASN cc_start: 0.9158 (t0) cc_final: 0.8483 (t0) REVERT: A 153 GLU cc_start: 0.8332 (mp0) cc_final: 0.7754 (mp0) REVERT: A 239 HIS cc_start: 0.8205 (t-170) cc_final: 0.7852 (t-170) REVERT: A 291 ILE cc_start: 0.6093 (OUTLIER) cc_final: 0.5760 (tt) REVERT: B 116 ARG cc_start: 0.7341 (mtm-85) cc_final: 0.6934 (mmm-85) REVERT: B 214 ARG cc_start: 0.7286 (mmt90) cc_final: 0.6532 (mmm-85) REVERT: B 222 ARG cc_start: 0.8422 (tmt170) cc_final: 0.8128 (tmt170) outliers start: 18 outliers final: 7 residues processed: 88 average time/residue: 0.1582 time to fit residues: 17.5421 Evaluate side-chains 73 residues out of total 438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 65 time to evaluate : 0.451 ------------------------------------------------------------------------------- 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 28 optimal weight: 6.9990 chunk 27 optimal weight: 3.9990 chunk 37 optimal weight: 2.9990 chunk 44 optimal weight: 0.7980 chunk 19 optimal weight: 0.7980 chunk 40 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 chunk 46 optimal weight: 8.9990 chunk 23 optimal weight: 0.3980 chunk 43 optimal weight: 2.9990 chunk 35 optimal weight: 5.9990 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.168147 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.116793 restraints weight = 4560.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.120166 restraints weight = 3194.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.122318 restraints weight = 2632.026| |-----------------------------------------------------------------------------| r_work (final): 0.3063 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7724 moved from start: 0.1420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 4121 Z= 0.329 Angle : 0.589 7.174 5595 Z= 0.298 Chirality : 0.044 0.132 606 Planarity : 0.004 0.033 713 Dihedral : 5.469 45.199 561 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.87 % Favored : 94.13 % Rotamer: Outliers : 5.71 % Allowed : 24.43 % 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: -0.86 (0.38), residues: 494 helix: 1.04 (0.38), residues: 190 sheet: -1.34 (0.68), residues: 44 loop : -1.73 (0.38), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 178 HIS 0.005 0.001 HIS B 212 PHE 0.011 0.001 PHE A 218 TYR 0.011 0.001 TYR B 200 ARG 0.002 0.000 ARG A 242 *********************** 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 94 residues out of total 438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 69 time to evaluate : 0.502 Fit side-chains REVERT: A 88 MET cc_start: 0.7413 (tmm) cc_final: 0.7132 (tmm) REVERT: A 152 GLN cc_start: 0.8159 (tp-100) cc_final: 0.7758 (tp-100) REVERT: A 153 GLU cc_start: 0.8396 (mp0) cc_final: 0.7815 (mp0) REVERT: A 239 HIS cc_start: 0.8425 (t-170) cc_final: 0.8215 (t-170) REVERT: A 291 ILE cc_start: 0.6088 (OUTLIER) cc_final: 0.5802 (tt) REVERT: B 116 ARG cc_start: 0.7472 (mtm-85) cc_final: 0.6989 (mmm-85) REVERT: B 205 ASN cc_start: 0.7489 (m-40) cc_final: 0.7099 (m-40) REVERT: B 218 LEU cc_start: 0.8725 (OUTLIER) cc_final: 0.8517 (tt) REVERT: B 222 ARG cc_start: 0.8368 (tmt170) cc_final: 0.8146 (tmt170) outliers start: 25 outliers final: 15 residues processed: 89 average time/residue: 0.1732 time to fit residues: 19.3989 Evaluate side-chains 82 residues out of total 438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 65 time to evaluate : 0.453 ------------------------------------------------------------------------------- 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 111 ILE Chi-restraints excluded: chain A residue 130 SER Chi-restraints excluded: chain A residue 166 ILE Chi-restraints excluded: chain A residue 243 GLU Chi-restraints excluded: chain A residue 262 LEU 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 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 218 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 30 optimal weight: 1.9990 chunk 41 optimal weight: 0.9980 chunk 6 optimal weight: 0.1980 chunk 35 optimal weight: 10.0000 chunk 18 optimal weight: 0.8980 chunk 27 optimal weight: 3.9990 chunk 42 optimal weight: 0.8980 chunk 36 optimal weight: 1.9990 chunk 31 optimal weight: 0.7980 chunk 46 optimal weight: 4.9990 chunk 20 optimal weight: 2.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.3865 r_free = 0.3865 target = 0.170994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.125534 restraints weight = 4534.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.127580 restraints weight = 3702.187| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.127712 restraints weight = 3148.952| |-----------------------------------------------------------------------------| r_work (final): 0.3144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7674 moved from start: 0.1830 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= 0.181 Angle : 0.522 7.616 5595 Z= 0.264 Chirality : 0.041 0.138 606 Planarity : 0.004 0.033 713 Dihedral : 4.911 33.845 561 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 4.57 % Allowed : 25.11 % 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: -0.29 (0.38), residues: 494 helix: 1.67 (0.39), residues: 183 sheet: -0.66 (0.80), residues: 34 loop : -1.51 (0.37), residues: 277 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 100 HIS 0.004 0.001 HIS B 212 PHE 0.009 0.001 PHE B 231 TYR 0.012 0.001 TYR B 200 ARG 0.002 0.000 ARG A 242 *********************** 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 88 residues out of total 438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 68 time to evaluate : 0.422 Fit side-chains REVERT: A 76 LEU cc_start: 0.9089 (OUTLIER) cc_final: 0.8757 (tt) REVERT: A 88 MET cc_start: 0.7292 (tmm) cc_final: 0.6994 (tmm) REVERT: A 152 GLN cc_start: 0.8078 (tp-100) cc_final: 0.7751 (tp-100) REVERT: A 153 GLU cc_start: 0.8312 (mp0) cc_final: 0.7768 (mp0) REVERT: A 239 HIS cc_start: 0.8435 (t-170) cc_final: 0.8224 (t-170) REVERT: B 116 ARG cc_start: 0.7646 (mtm-85) cc_final: 0.7232 (mmm-85) REVERT: B 205 ASN cc_start: 0.7823 (m-40) cc_final: 0.7445 (m-40) outliers start: 20 outliers final: 14 residues processed: 82 average time/residue: 0.1504 time to fit residues: 15.7328 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 : 0.402 ------------------------------------------------------------------------------- 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 243 GLU Chi-restraints excluded: chain A residue 258 CYS 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 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 232 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 39 optimal weight: 1.9990 chunk 19 optimal weight: 0.7980 chunk 34 optimal weight: 1.9990 chunk 38 optimal weight: 0.7980 chunk 42 optimal weight: 0.9990 chunk 26 optimal weight: 4.9990 chunk 10 optimal weight: 0.8980 chunk 40 optimal weight: 0.8980 chunk 28 optimal weight: 5.9990 chunk 27 optimal weight: 2.9990 chunk 7 optimal weight: 0.9990 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.170714 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.125182 restraints weight = 4586.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.127615 restraints weight = 3582.419| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.127637 restraints weight = 2994.579| |-----------------------------------------------------------------------------| r_work (final): 0.3147 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7647 moved from start: 0.2003 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= 0.203 Angle : 0.515 5.968 5595 Z= 0.262 Chirality : 0.041 0.136 606 Planarity : 0.004 0.034 713 Dihedral : 4.837 33.344 561 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 3.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 4.34 % Allowed : 24.66 % 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: -0.16 (0.38), residues: 494 helix: 1.80 (0.39), residues: 184 sheet: -0.56 (0.78), residues: 34 loop : -1.46 (0.37), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 178 HIS 0.003 0.001 HIS B 212 PHE 0.009 0.001 PHE B 231 TYR 0.010 0.001 TYR A 115 ARG 0.002 0.000 ARG B 214 *********************** 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 84 residues out of total 438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 65 time to evaluate : 0.444 Fit side-chains REVERT: A 76 LEU cc_start: 0.9092 (OUTLIER) cc_final: 0.8719 (tt) REVERT: A 88 MET cc_start: 0.7330 (tmm) cc_final: 0.7042 (tmm) REVERT: A 152 GLN cc_start: 0.8072 (tp-100) cc_final: 0.7711 (tp-100) REVERT: A 153 GLU cc_start: 0.8302 (mp0) cc_final: 0.7770 (mp0) REVERT: A 291 ILE cc_start: 0.6271 (OUTLIER) cc_final: 0.5995 (tt) REVERT: B 116 ARG cc_start: 0.7751 (mtm-85) cc_final: 0.7280 (mmm-85) REVERT: B 205 ASN cc_start: 0.7820 (m-40) cc_final: 0.7383 (m-40) outliers start: 19 outliers final: 13 residues processed: 79 average time/residue: 0.1340 time to fit residues: 13.8222 Evaluate side-chains 74 residues out of total 438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 59 time to evaluate : 0.403 ------------------------------------------------------------------------------- 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 318 MET 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 40 optimal weight: 2.9990 chunk 47 optimal weight: 2.9990 chunk 39 optimal weight: 4.9990 chunk 30 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 4 optimal weight: 0.5980 chunk 7 optimal weight: 4.9990 chunk 12 optimal weight: 0.9980 chunk 18 optimal weight: 0.9980 chunk 10 optimal weight: 0.9990 chunk 15 optimal weight: 0.5980 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.169268 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.122479 restraints weight = 4529.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.124400 restraints weight = 3418.032| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.124753 restraints weight = 2796.241| |-----------------------------------------------------------------------------| r_work (final): 0.3129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7737 moved from start: 0.2136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4121 Z= 0.198 Angle : 0.552 8.864 5595 Z= 0.272 Chirality : 0.041 0.133 606 Planarity : 0.004 0.034 713 Dihedral : 4.808 33.774 561 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 5.02 % Allowed : 24.66 % 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: 0.00 (0.38), residues: 494 helix: 1.93 (0.39), residues: 184 sheet: -0.49 (0.77), residues: 34 loop : -1.36 (0.37), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 178 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 0.002 0.000 ARG A 242 *********************** 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 86 residues out of total 438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 64 time to evaluate : 0.407 Fit side-chains REVERT: A 76 LEU cc_start: 0.9098 (OUTLIER) cc_final: 0.8738 (tt) REVERT: A 88 MET cc_start: 0.7424 (tmm) cc_final: 0.7127 (tmm) REVERT: A 152 GLN cc_start: 0.8057 (tp-100) cc_final: 0.7748 (tp-100) REVERT: A 153 GLU cc_start: 0.8260 (mp0) cc_final: 0.7785 (mp0) REVERT: A 291 ILE cc_start: 0.6304 (OUTLIER) cc_final: 0.6024 (tt) REVERT: B 116 ARG cc_start: 0.7626 (mtm-85) cc_final: 0.7245 (mmm-85) REVERT: B 205 ASN cc_start: 0.7962 (m-40) cc_final: 0.7570 (m-40) outliers start: 22 outliers final: 15 residues processed: 81 average time/residue: 0.1377 time to fit residues: 14.3580 Evaluate side-chains 79 residues out of total 438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 62 time to evaluate : 0.403 ------------------------------------------------------------------------------- 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 318 MET 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 19 optimal weight: 0.9980 chunk 10 optimal weight: 0.5980 chunk 34 optimal weight: 0.1980 chunk 20 optimal weight: 2.9990 chunk 12 optimal weight: 0.9990 chunk 14 optimal weight: 0.9990 chunk 44 optimal weight: 0.8980 chunk 16 optimal weight: 0.9980 chunk 25 optimal weight: 0.2980 chunk 26 optimal weight: 5.9990 chunk 22 optimal weight: 20.0000 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 = 0.3881 r_free = 0.3881 target = 0.172542 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.126984 restraints weight = 4539.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.129363 restraints weight = 3554.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.129414 restraints weight = 2976.908| |-----------------------------------------------------------------------------| r_work (final): 0.3164 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7675 moved from start: 0.2325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 4121 Z= 0.161 Angle : 0.520 8.297 5595 Z= 0.259 Chirality : 0.040 0.134 606 Planarity : 0.004 0.035 713 Dihedral : 4.641 33.493 561 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 3.20 % Allowed : 26.26 % 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: 0.17 (0.38), residues: 494 helix: 2.09 (0.38), residues: 184 sheet: -0.46 (0.78), residues: 34 loop : -1.27 (0.37), residues: 276 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 0.016 0.001 TYR B 200 ARG 0.002 0.000 ARG B 113 *********************** 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 79 residues out of total 438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 65 time to evaluate : 0.405 Fit side-chains REVERT: A 76 LEU cc_start: 0.9075 (OUTLIER) cc_final: 0.8752 (tt) REVERT: A 88 MET cc_start: 0.7235 (tmm) cc_final: 0.6966 (tmm) REVERT: A 152 GLN cc_start: 0.8109 (tp-100) cc_final: 0.7779 (tp-100) REVERT: A 153 GLU cc_start: 0.8215 (mp0) cc_final: 0.7743 (mp0) REVERT: B 116 ARG cc_start: 0.7717 (mtm-85) cc_final: 0.7447 (mmm-85) REVERT: B 205 ASN cc_start: 0.7969 (m-40) cc_final: 0.7561 (m-40) outliers start: 14 outliers final: 13 residues processed: 74 average time/residue: 0.1363 time to fit residues: 13.1852 Evaluate side-chains 76 residues out of total 438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 62 time to evaluate : 0.401 ------------------------------------------------------------------------------- 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 318 MET 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 232 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 22 optimal weight: 0.0980 chunk 6 optimal weight: 1.9990 chunk 35 optimal weight: 0.3980 chunk 36 optimal weight: 9.9990 chunk 21 optimal weight: 0.8980 chunk 24 optimal weight: 2.9990 chunk 8 optimal weight: 0.9980 chunk 2 optimal weight: 6.9990 chunk 43 optimal weight: 2.9990 chunk 25 optimal weight: 0.9990 chunk 47 optimal weight: 0.5980 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 = 0.3884 r_free = 0.3884 target = 0.172762 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.127573 restraints weight = 4475.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.129855 restraints weight = 3520.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.129922 restraints weight = 2996.446| |-----------------------------------------------------------------------------| r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7675 moved from start: 0.2427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 4121 Z= 0.165 Angle : 0.543 9.284 5595 Z= 0.264 Chirality : 0.040 0.133 606 Planarity : 0.004 0.035 713 Dihedral : 4.555 32.263 561 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 3.65 % Allowed : 26.48 % 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: 0.29 (0.38), residues: 494 helix: 2.19 (0.39), residues: 184 sheet: -0.37 (0.78), residues: 34 loop : -1.21 (0.37), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 178 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 0.002 0.000 ARG B 113 *********************** 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 82 residues out of total 438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 66 time to evaluate : 0.444 Fit side-chains REVERT: A 76 LEU cc_start: 0.9121 (OUTLIER) cc_final: 0.8772 (tt) REVERT: A 88 MET cc_start: 0.7285 (tmm) cc_final: 0.7018 (tmm) REVERT: A 152 GLN cc_start: 0.8036 (tp-100) cc_final: 0.7751 (tp-100) REVERT: B 116 ARG cc_start: 0.7714 (mtm-85) cc_final: 0.7477 (mmm-85) REVERT: B 198 GLU cc_start: 0.8678 (OUTLIER) cc_final: 0.8391 (mt-10) REVERT: B 205 ASN cc_start: 0.7814 (m-40) cc_final: 0.7589 (m-40) outliers start: 16 outliers final: 13 residues processed: 76 average time/residue: 0.1389 time to fit residues: 13.8353 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 : 0.424 ------------------------------------------------------------------------------- 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 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 198 GLU 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 24 optimal weight: 3.9990 chunk 47 optimal weight: 3.9990 chunk 15 optimal weight: 0.9980 chunk 14 optimal weight: 0.9990 chunk 22 optimal weight: 6.9990 chunk 35 optimal weight: 1.9990 chunk 32 optimal weight: 0.7980 chunk 21 optimal weight: 0.7980 chunk 9 optimal weight: 3.9990 chunk 13 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- 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 = 0.3862 r_free = 0.3862 target = 0.170464 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.124376 restraints weight = 4553.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.127255 restraints weight = 3620.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.127188 restraints weight = 2959.457| |-----------------------------------------------------------------------------| r_work (final): 0.3139 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7712 moved from start: 0.2307 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= 0.243 Angle : 0.558 9.288 5595 Z= 0.277 Chirality : 0.042 0.132 606 Planarity : 0.004 0.034 713 Dihedral : 4.723 33.758 561 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % 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: 0.19 (0.38), residues: 494 helix: 2.04 (0.38), residues: 184 sheet: -0.35 (0.79), residues: 34 loop : -1.21 (0.38), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 178 HIS 0.012 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 B 222 *********************** 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 84 residues out of total 438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 67 time to evaluate : 0.511 Fit side-chains REVERT: A 76 LEU cc_start: 0.9142 (OUTLIER) cc_final: 0.8779 (tt) REVERT: A 88 MET cc_start: 0.7339 (tmm) cc_final: 0.7067 (tmm) REVERT: A 152 GLN cc_start: 0.8066 (tp-100) cc_final: 0.7725 (tp-100) REVERT: A 153 GLU cc_start: 0.8309 (mp0) cc_final: 0.7604 (mp0) REVERT: A 291 ILE cc_start: 0.6303 (OUTLIER) cc_final: 0.6073 (tt) REVERT: B 116 ARG cc_start: 0.7835 (mtm-85) cc_final: 0.7584 (mmm-85) REVERT: B 198 GLU cc_start: 0.8686 (OUTLIER) cc_final: 0.8408 (mt-10) REVERT: B 205 ASN cc_start: 0.7960 (m-40) cc_final: 0.7689 (m-40) outliers start: 17 outliers final: 13 residues processed: 79 average time/residue: 0.1413 time to fit residues: 15.5365 Evaluate side-chains 79 residues out of total 438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 63 time to evaluate : 0.399 ------------------------------------------------------------------------------- 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 198 GLU 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 45 optimal weight: 4.9990 chunk 27 optimal weight: 1.9990 chunk 47 optimal weight: 0.9990 chunk 34 optimal weight: 2.9990 chunk 22 optimal weight: 10.0000 chunk 40 optimal weight: 0.6980 chunk 5 optimal weight: 0.0030 chunk 14 optimal weight: 0.9990 chunk 0 optimal weight: 2.9990 chunk 11 optimal weight: 0.9980 chunk 19 optimal weight: 0.4980 overall best weight: 0.6392 ------------------------------------------------------------------------------- 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 = 0.3909 r_free = 0.3909 target = 0.174841 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.129132 restraints weight = 4620.312| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.131933 restraints weight = 4489.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.133321 restraints weight = 3067.366| |-----------------------------------------------------------------------------| r_work (final): 0.3172 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7707 moved from start: 0.2456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4121 Z= 0.177 Angle : 0.564 9.235 5595 Z= 0.276 Chirality : 0.041 0.134 606 Planarity : 0.004 0.034 713 Dihedral : 4.608 32.562 561 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 3.20 % Allowed : 26.94 % 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: 0.35 (0.39), residues: 494 helix: 2.19 (0.38), residues: 184 sheet: -0.28 (0.79), residues: 34 loop : -1.14 (0.38), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 100 HIS 0.012 0.001 HIS A 239 PHE 0.010 0.001 PHE B 231 TYR 0.010 0.001 TYR A 115 ARG 0.002 0.000 ARG B 113 ********************** 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 78 residues out of total 438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 64 time to evaluate : 0.438 Fit side-chains REVERT: A 76 LEU cc_start: 0.9089 (OUTLIER) cc_final: 0.8757 (tt) REVERT: A 88 MET cc_start: 0.7420 (tmm) cc_final: 0.7150 (tmm) REVERT: A 152 GLN cc_start: 0.8026 (tp-100) cc_final: 0.7717 (tp-100) REVERT: A 153 GLU cc_start: 0.8258 (mp0) cc_final: 0.7644 (mp0) REVERT: B 116 ARG cc_start: 0.7568 (mtm-85) cc_final: 0.7313 (mmm-85) REVERT: B 198 GLU cc_start: 0.8644 (OUTLIER) cc_final: 0.8422 (mt-10) REVERT: B 205 ASN cc_start: 0.7908 (m-40) cc_final: 0.7642 (m-40) outliers start: 14 outliers final: 12 residues processed: 74 average time/residue: 0.2143 time to fit residues: 20.3015 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 : 0.421 ------------------------------------------------------------------------------- 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 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 198 GLU Chi-restraints excluded: chain B residue 232 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/iotbx/cli_parser.py", line 980, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 64.3048 > 50: distance: 85 - 104: 29.542 distance: 90 - 95: 28.798 distance: 95 - 96: 24.360 distance: 96 - 97: 46.570 distance: 97 - 98: 25.107 distance: 97 - 99: 46.313 distance: 99 - 100: 21.022 distance: 100 - 101: 11.367 distance: 100 - 103: 34.758 distance: 101 - 102: 35.032 distance: 101 - 105: 12.155 distance: 103 - 104: 53.812 distance: 106 - 107: 17.832 distance: 106 - 109: 22.925 distance: 107 - 108: 22.827 distance: 107 - 111: 41.761 distance: 109 - 110: 27.210 distance: 111 - 112: 14.675 distance: 112 - 113: 44.762 distance: 112 - 115: 35.246 distance: 113 - 117: 40.524 distance: 115 - 116: 48.262 distance: 117 - 118: 33.340 distance: 118 - 119: 9.483 distance: 118 - 121: 15.437 distance: 119 - 120: 42.426 distance: 119 - 124: 25.960 distance: 121 - 122: 15.163 distance: 121 - 123: 13.774 distance: 124 - 125: 42.133 distance: 125 - 126: 42.372 distance: 125 - 128: 53.474 distance: 126 - 127: 42.907 distance: 126 - 130: 41.037 distance: 127 - 145: 51.073 distance: 128 - 129: 9.867 distance: 130 - 131: 42.836 distance: 130 - 136: 43.652 distance: 131 - 132: 30.919 distance: 131 - 134: 49.968 distance: 132 - 133: 31.200 distance: 132 - 137: 33.209 distance: 133 - 151: 23.055 distance: 134 - 135: 54.239 distance: 135 - 136: 14.578 distance: 137 - 138: 13.945 distance: 138 - 139: 21.351 distance: 138 - 141: 22.226 distance: 139 - 140: 23.444 distance: 139 - 145: 13.372 distance: 140 - 160: 20.082 distance: 141 - 142: 19.844 distance: 142 - 143: 9.287 distance: 142 - 144: 11.302 distance: 145 - 146: 4.073 distance: 146 - 147: 51.417 distance: 146 - 149: 21.316 distance: 147 - 148: 35.734 distance: 147 - 151: 55.379 distance: 149 - 150: 46.406 distance: 151 - 152: 30.604 distance: 152 - 153: 25.392 distance: 152 - 155: 28.967 distance: 153 - 154: 12.007 distance: 153 - 160: 27.081 distance: 155 - 156: 21.707 distance: 156 - 157: 33.548 distance: 157 - 158: 11.508 distance: 157 - 159: 22.387