Starting phenix.real_space_refine on Sun Apr 27 01:37:53 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hfc_34717/04_2025/8hfc_34717.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hfc_34717/04_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_34717/04_2025/8hfc_34717.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hfc_34717/04_2025/8hfc_34717.map" model { file = "/net/cci-nas-00/data/ceres_data/8hfc_34717/04_2025/8hfc_34717.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hfc_34717/04_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-5669/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: 3.04, per 1000 atoms: 0.76 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: 1.04 Conformation dependent library (CDL) restraints added in 470.4 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: 0.38 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: 0.93 Time building geometry restraints manager: 1.24 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: 0.780 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: 15.020 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.200 ------------------------------------------------------------------------------- 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 : 0.008 0.121 4131 Z= 0.315 Angle : 0.781 19.255 5603 Z= 0.385 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 Details of bonding type rmsd hydrogen bonds : bond 0.11184 ( 160) hydrogen bonds : angle 5.51198 ( 435) metal coordination : bond 0.06666 ( 8) metal coordination : angle 12.21092 ( 6) SS BOND : bond 0.00046 ( 1) SS BOND : angle 0.60188 ( 2) covalent geometry : bond 0.00699 ( 4121) covalent geometry : angle 0.67102 ( 5595) Misc. bond : bond 0.03646 ( 1) *********************** 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 : 0.406 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: 0.1647 time to fit residues: 16.7473 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 : 0.401 ------------------------------------------------------------------------------- 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 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 4131 Z= 0.096 Angle : 0.529 6.755 5603 Z= 0.275 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 Details of bonding type rmsd hydrogen bonds : bond 0.03770 ( 160) hydrogen bonds : angle 4.30917 ( 435) metal coordination : bond 0.00502 ( 8) metal coordination : angle 2.22770 ( 6) SS BOND : bond 0.00176 ( 1) SS BOND : angle 0.18716 ( 2) covalent geometry : bond 0.00201 ( 4121) covalent geometry : angle 0.52430 ( 5595) Misc. bond : bond 0.00035 ( 1) *********************** 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 : 0.401 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: 0.1478 time to fit residues: 16.4162 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 : 0.408 ------------------------------------------------------------------------------- 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 4131 Z= 0.206 Angle : 0.597 7.174 5603 Z= 0.299 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 Details of bonding type rmsd hydrogen bonds : bond 0.04559 ( 160) hydrogen bonds : angle 4.26205 ( 435) metal coordination : bond 0.01563 ( 8) metal coordination : angle 2.90755 ( 6) SS BOND : bond 0.00238 ( 1) SS BOND : angle 0.95877 ( 2) covalent geometry : bond 0.00508 ( 4121) covalent geometry : angle 0.58927 ( 5595) Misc. bond : bond 0.00006 ( 1) *********************** 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 : 0.427 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: 0.1629 time to fit residues: 17.9746 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 : 0.450 ------------------------------------------------------------------------------- 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 4131 Z= 0.119 Angle : 0.525 7.616 5603 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 Details of bonding type rmsd hydrogen bonds : bond 0.03772 ( 160) hydrogen bonds : angle 3.93216 ( 435) metal coordination : bond 0.00724 ( 8) metal coordination : angle 1.84889 ( 6) SS BOND : bond 0.00220 ( 1) SS BOND : angle 0.16532 ( 2) covalent geometry : bond 0.00278 ( 4121) covalent geometry : angle 0.52161 ( 5595) Misc. bond : bond 0.00005 ( 1) *********************** 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 : 0.455 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: 0.1487 time to fit residues: 15.5852 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 : 0.471 ------------------------------------------------------------------------------- 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 4131 Z= 0.130 Angle : 0.518 5.968 5603 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 Details of bonding type rmsd hydrogen bonds : bond 0.03729 ( 160) hydrogen bonds : angle 3.84625 ( 435) metal coordination : bond 0.00846 ( 8) metal coordination : angle 1.89389 ( 6) SS BOND : bond 0.00107 ( 1) SS BOND : angle 0.07050 ( 2) covalent geometry : bond 0.00312 ( 4121) covalent geometry : angle 0.51474 ( 5595) Misc. bond : bond 0.00005 ( 1) *********************** 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 : 0.447 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: 0.1304 time to fit residues: 13.4708 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 : 0.399 ------------------------------------------------------------------------------- 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 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: 2.9990 chunk 18 optimal weight: 0.9980 chunk 10 optimal weight: 0.9980 chunk 15 optimal weight: 0.5980 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** B 68 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.170466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.124675 restraints weight = 4548.422| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.127005 restraints weight = 3626.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.127041 restraints weight = 3039.262| |-----------------------------------------------------------------------------| r_work (final): 0.3131 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7722 moved from start: 0.2087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 4131 Z= 0.145 Angle : 0.567 9.075 5603 Z= 0.278 Chirality : 0.042 0.133 606 Planarity : 0.004 0.034 713 Dihedral : 4.882 33.650 561 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % 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: -0.05 (0.38), residues: 494 helix: 1.88 (0.38), residues: 184 sheet: -0.50 (0.78), residues: 34 loop : -1.39 (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 0.011 0.001 TYR A 115 ARG 0.002 0.000 ARG A 242 Details of bonding type rmsd hydrogen bonds : bond 0.03870 ( 160) hydrogen bonds : angle 3.88723 ( 435) metal coordination : bond 0.00907 ( 8) metal coordination : angle 1.92030 ( 6) SS BOND : bond 0.00742 ( 1) SS BOND : angle 1.09702 ( 2) covalent geometry : bond 0.00354 ( 4121) covalent geometry : angle 0.56348 ( 5595) Misc. bond : bond 0.00005 ( 1) *********************** 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 85 residues out of total 438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 63 time to evaluate : 0.405 Fit side-chains REVERT: A 76 LEU cc_start: 0.9101 (OUTLIER) cc_final: 0.8733 (tt) REVERT: A 88 MET cc_start: 0.7406 (tmm) cc_final: 0.7118 (tmm) REVERT: A 152 GLN cc_start: 0.8062 (tp-100) cc_final: 0.7751 (tp-100) REVERT: A 153 GLU cc_start: 0.8270 (mp0) cc_final: 0.7796 (mp0) REVERT: A 291 ILE cc_start: 0.6313 (OUTLIER) cc_final: 0.6035 (tt) REVERT: B 116 ARG cc_start: 0.7621 (mtm-85) cc_final: 0.7229 (mmm-85) REVERT: B 205 ASN cc_start: 0.7971 (m-40) cc_final: 0.7578 (m-40) outliers start: 22 outliers final: 16 residues processed: 80 average time/residue: 0.1376 time to fit residues: 14.3374 Evaluate side-chains 80 residues out of total 438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 62 time to evaluate : 0.406 ------------------------------------------------------------------------------- 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 156 GLU 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: 0.6980 chunk 34 optimal weight: 0.0020 chunk 20 optimal weight: 2.9990 chunk 12 optimal weight: 0.9990 chunk 14 optimal weight: 0.4980 chunk 44 optimal weight: 3.9990 chunk 16 optimal weight: 2.9990 chunk 25 optimal weight: 0.0050 chunk 26 optimal weight: 0.9990 chunk 22 optimal weight: 0.0470 overall best weight: 0.2500 ------------------------------------------------------------------------------- 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 = 0.3904 r_free = 0.3904 target = 0.174979 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.130015 restraints weight = 4521.062| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.132444 restraints weight = 3575.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.132505 restraints weight = 3038.311| |-----------------------------------------------------------------------------| r_work (final): 0.3196 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7660 moved from start: 0.2488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 4131 Z= 0.089 Angle : 0.510 8.113 5603 Z= 0.255 Chirality : 0.040 0.126 606 Planarity : 0.004 0.035 713 Dihedral : 4.495 33.013 561 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 2.28 % Allowed : 26.94 % Favored : 70.78 % 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: 0.25 (0.38), residues: 494 helix: 2.21 (0.38), residues: 184 sheet: -0.42 (0.79), residues: 34 loop : -1.26 (0.37), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 100 HIS 0.010 0.001 HIS A 239 PHE 0.009 0.001 PHE A 287 TYR 0.015 0.001 TYR B 200 ARG 0.004 0.000 ARG B 113 Details of bonding type rmsd hydrogen bonds : bond 0.03109 ( 160) hydrogen bonds : angle 3.70136 ( 435) metal coordination : bond 0.00403 ( 8) metal coordination : angle 1.47423 ( 6) SS BOND : bond 0.00495 ( 1) SS BOND : angle 0.33086 ( 2) covalent geometry : bond 0.00190 ( 4121) covalent geometry : angle 0.50830 ( 5595) Misc. bond : bond 0.00007 ( 1) *********************** 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: 10 poor density : 69 time to evaluate : 0.333 Fit side-chains REVERT: A 88 MET cc_start: 0.7285 (tmm) cc_final: 0.7013 (tmm) REVERT: A 152 GLN cc_start: 0.8080 (tp-100) cc_final: 0.7771 (tp-100) REVERT: A 153 GLU cc_start: 0.8185 (mp0) cc_final: 0.7714 (mp0) REVERT: A 321 LEU cc_start: 0.8687 (OUTLIER) cc_final: 0.8430 (tm) REVERT: B 69 VAL cc_start: 0.8968 (t) cc_final: 0.8737 (p) REVERT: B 116 ARG cc_start: 0.7679 (mtm-85) cc_final: 0.7465 (mmm-85) REVERT: B 171 ASP cc_start: 0.8404 (t0) cc_final: 0.8041 (t0) REVERT: B 205 ASN cc_start: 0.7830 (m-40) cc_final: 0.7555 (m-40) outliers start: 10 outliers final: 8 residues processed: 75 average time/residue: 0.1455 time to fit residues: 13.9797 Evaluate side-chains 75 residues out of total 438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 66 time to evaluate : 0.441 ------------------------------------------------------------------------------- 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 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: 0.0870 chunk 6 optimal weight: 0.0970 chunk 35 optimal weight: 0.9990 chunk 36 optimal weight: 8.9990 chunk 21 optimal weight: 0.6980 chunk 24 optimal weight: 2.9990 chunk 8 optimal weight: 0.9980 chunk 2 optimal weight: 3.9990 chunk 43 optimal weight: 3.9990 chunk 25 optimal weight: 0.9980 chunk 47 optimal weight: 1.9990 overall best weight: 0.5756 ------------------------------------------------------------------------------- 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 = 0.3926 r_free = 0.3926 target = 0.176624 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.125939 restraints weight = 4603.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.129524 restraints weight = 3199.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.132004 restraints weight = 2612.259| |-----------------------------------------------------------------------------| r_work (final): 0.3148 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7703 moved from start: 0.2490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4131 Z= 0.106 Angle : 0.552 9.279 5603 Z= 0.269 Chirality : 0.040 0.132 606 Planarity : 0.004 0.035 713 Dihedral : 4.472 31.799 561 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 2.28 % Allowed : 27.17 % 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: 0.34 (0.39), residues: 494 helix: 2.31 (0.39), residues: 184 sheet: -0.39 (0.79), residues: 34 loop : -1.22 (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 Details of bonding type rmsd hydrogen bonds : bond 0.03291 ( 160) hydrogen bonds : angle 3.67228 ( 435) metal coordination : bond 0.00644 ( 8) metal coordination : angle 1.58110 ( 6) SS BOND : bond 0.00256 ( 1) SS BOND : angle 0.14272 ( 2) covalent geometry : bond 0.00253 ( 4121) covalent geometry : angle 0.55043 ( 5595) Misc. bond : bond 0.00010 ( 1) *********************** 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 77 residues out of total 438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 67 time to evaluate : 0.418 Fit side-chains REVERT: A 88 MET cc_start: 0.7233 (tmm) cc_final: 0.6969 (tmm) REVERT: A 152 GLN cc_start: 0.8044 (tp-100) cc_final: 0.7673 (tp-100) REVERT: A 153 GLU cc_start: 0.8213 (mp0) cc_final: 0.7746 (mp0) REVERT: B 69 VAL cc_start: 0.8942 (t) cc_final: 0.8717 (p) REVERT: B 116 ARG cc_start: 0.7620 (mtm-85) cc_final: 0.7342 (mmm-85) REVERT: B 198 GLU cc_start: 0.8697 (OUTLIER) cc_final: 0.8357 (mt-10) REVERT: B 205 ASN cc_start: 0.7752 (m-40) cc_final: 0.7495 (m-40) outliers start: 10 outliers final: 9 residues processed: 73 average time/residue: 0.1895 time to fit residues: 18.0294 Evaluate side-chains 76 residues out of total 438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 66 time to evaluate : 0.641 ------------------------------------------------------------------------------- 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 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 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: 0.4980 chunk 15 optimal weight: 0.6980 chunk 14 optimal weight: 1.9990 chunk 22 optimal weight: 4.9990 chunk 35 optimal weight: 2.9990 chunk 32 optimal weight: 0.9980 chunk 21 optimal weight: 0.9980 chunk 9 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.171256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.125482 restraints weight = 4552.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.128122 restraints weight = 3590.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.128118 restraints weight = 2978.660| |-----------------------------------------------------------------------------| r_work (final): 0.3148 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7703 moved from start: 0.2389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4131 Z= 0.142 Angle : 0.551 9.273 5603 Z= 0.272 Chirality : 0.042 0.136 606 Planarity : 0.004 0.034 713 Dihedral : 4.665 33.456 561 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 2.97 % Allowed : 27.40 % 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: 0.20 (0.39), residues: 494 helix: 2.16 (0.38), residues: 184 sheet: -0.83 (0.69), residues: 44 loop : -1.22 (0.38), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 178 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 222 Details of bonding type rmsd hydrogen bonds : bond 0.03729 ( 160) hydrogen bonds : angle 3.76435 ( 435) metal coordination : bond 0.00863 ( 8) metal coordination : angle 1.94690 ( 6) SS BOND : bond 0.00213 ( 1) SS BOND : angle 0.11231 ( 2) covalent geometry : bond 0.00348 ( 4121) covalent geometry : angle 0.54736 ( 5595) Misc. bond : bond 0.00006 ( 1) *********************** 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: 13 poor density : 66 time to evaluate : 0.472 Fit side-chains REVERT: A 88 MET cc_start: 0.7311 (tmm) cc_final: 0.7051 (tmm) REVERT: A 152 GLN cc_start: 0.8036 (tp-100) cc_final: 0.7756 (tp-100) REVERT: B 69 VAL cc_start: 0.8950 (t) cc_final: 0.8729 (p) REVERT: B 116 ARG cc_start: 0.7780 (mtm-85) cc_final: 0.7542 (mmm-85) REVERT: B 198 GLU cc_start: 0.8685 (OUTLIER) cc_final: 0.8410 (mt-10) REVERT: B 205 ASN cc_start: 0.7944 (m-40) cc_final: 0.7677 (m-40) outliers start: 13 outliers final: 12 residues processed: 74 average time/residue: 0.1413 time to fit residues: 13.6340 Evaluate side-chains 76 residues out of total 438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 63 time to evaluate : 0.459 ------------------------------------------------------------------------------- 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 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 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: 2.9990 chunk 47 optimal weight: 0.9980 chunk 34 optimal weight: 0.9980 chunk 22 optimal weight: 8.9990 chunk 40 optimal weight: 0.6980 chunk 5 optimal weight: 0.5980 chunk 14 optimal weight: 0.9990 chunk 0 optimal weight: 2.9990 chunk 11 optimal weight: 0.5980 chunk 19 optimal weight: 0.3980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 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 = 0.3910 r_free = 0.3910 target = 0.175323 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.124413 restraints weight = 4636.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.128198 restraints weight = 3204.703| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.130554 restraints weight = 2595.390| |-----------------------------------------------------------------------------| r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7734 moved from start: 0.2519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 4131 Z= 0.112 Angle : 0.555 9.453 5603 Z= 0.270 Chirality : 0.041 0.136 606 Planarity : 0.004 0.034 713 Dihedral : 4.519 32.461 561 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % 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: 0.36 (0.39), residues: 494 helix: 2.24 (0.38), residues: 184 sheet: -0.34 (0.80), residues: 34 loop : -1.15 (0.38), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 178 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 0.001 0.000 ARG A 242 Details of bonding type rmsd hydrogen bonds : bond 0.03382 ( 160) hydrogen bonds : angle 3.72437 ( 435) metal coordination : bond 0.00615 ( 8) metal coordination : angle 1.62955 ( 6) SS BOND : bond 0.00198 ( 1) SS BOND : angle 0.08265 ( 2) covalent geometry : bond 0.00268 ( 4121) covalent geometry : angle 0.55285 ( 5595) Misc. bond : bond 0.00003 ( 1) ********************** 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: 12 poor density : 66 time to evaluate : 0.445 Fit side-chains REVERT: A 88 MET cc_start: 0.7425 (tmm) cc_final: 0.7154 (tmm) REVERT: A 152 GLN cc_start: 0.8050 (tp-100) cc_final: 0.7678 (tp-100) REVERT: A 153 GLU cc_start: 0.8291 (mp0) cc_final: 0.7563 (mp0) REVERT: B 69 VAL cc_start: 0.8943 (t) cc_final: 0.8731 (p) REVERT: B 116 ARG cc_start: 0.7728 (mtm-85) cc_final: 0.7499 (mmm-85) REVERT: B 198 GLU cc_start: 0.8662 (OUTLIER) cc_final: 0.8369 (mt-10) REVERT: B 205 ASN cc_start: 0.7801 (m-40) cc_final: 0.7559 (m-40) outliers start: 12 outliers final: 11 residues processed: 73 average time/residue: 0.1382 time to fit residues: 13.1006 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 : 0.445 ------------------------------------------------------------------------------- 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 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 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-5669/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-5669/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/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-5669/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/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-5669/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-5669/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-5669/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-5669/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-5669/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-5669/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-5669/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-5669/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/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-5669/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-5669/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-5669/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-5669/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: 66.6253 > 50: distance: 85 - 104: 23.291 distance: 90 - 95: 35.940 distance: 95 - 96: 45.607 distance: 96 - 97: 27.846 distance: 97 - 98: 25.364 distance: 97 - 99: 22.892 distance: 99 - 100: 34.985 distance: 100 - 101: 37.356 distance: 100 - 103: 58.193 distance: 101 - 102: 40.324 distance: 101 - 105: 27.143 distance: 103 - 104: 43.388 distance: 105 - 106: 21.365 distance: 106 - 107: 21.868 distance: 106 - 109: 37.856 distance: 107 - 108: 13.651 distance: 107 - 111: 44.445 distance: 109 - 110: 45.501 distance: 111 - 112: 31.179 distance: 112 - 113: 16.225 distance: 112 - 115: 51.159 distance: 113 - 114: 30.145 distance: 113 - 117: 38.217 distance: 115 - 116: 56.889 distance: 117 - 118: 28.890 distance: 118 - 119: 40.811 distance: 118 - 121: 56.693 distance: 119 - 120: 28.853 distance: 119 - 124: 13.558 distance: 121 - 122: 40.179 distance: 121 - 123: 40.248 distance: 124 - 125: 15.029 distance: 125 - 126: 44.085 distance: 125 - 128: 52.663 distance: 126 - 127: 51.992 distance: 126 - 130: 51.516 distance: 127 - 145: 13.093 distance: 128 - 129: 57.602 distance: 130 - 131: 43.927 distance: 130 - 136: 45.090 distance: 131 - 132: 47.122 distance: 131 - 134: 57.039 distance: 132 - 133: 48.231 distance: 132 - 137: 26.722 distance: 133 - 151: 44.918 distance: 134 - 135: 56.169 distance: 135 - 136: 62.220 distance: 137 - 138: 11.899 distance: 138 - 139: 24.555 distance: 138 - 141: 36.331 distance: 139 - 140: 24.896 distance: 139 - 145: 17.493 distance: 140 - 160: 28.440 distance: 141 - 142: 14.566 distance: 142 - 143: 20.552 distance: 142 - 144: 25.663 distance: 145 - 146: 25.591 distance: 146 - 147: 42.852 distance: 146 - 149: 35.166 distance: 147 - 148: 53.036 distance: 147 - 151: 47.836 distance: 149 - 150: 33.335 distance: 151 - 152: 38.130 distance: 152 - 153: 40.299 distance: 152 - 155: 47.055 distance: 153 - 154: 41.792 distance: 153 - 160: 20.733 distance: 155 - 156: 40.074 distance: 156 - 157: 35.606 distance: 157 - 158: 8.949 distance: 157 - 159: 11.488