Starting phenix.real_space_refine on Sun Mar 10 18:33:50 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hfc_34717/03_2024/8hfc_34717_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hfc_34717/03_2024/8hfc_34717.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hfc_34717/03_2024/8hfc_34717.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hfc_34717/03_2024/8hfc_34717.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hfc_34717/03_2024/8hfc_34717_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hfc_34717/03_2024/8hfc_34717_updated.pdb" } 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 Residue "A ARG 145": "NH1" <-> "NH2" Residue "A GLU 153": "OE1" <-> "OE2" Residue "A ARG 242": "NH1" <-> "NH2" Residue "A GLU 243": "OE1" <-> "OE2" Residue "A GLU 305": "OE1" <-> "OE2" Residue "A GLU 306": "OE1" <-> "OE2" Residue "B GLU 25": "OE1" <-> "OE2" Residue "B GLU 32": "OE1" <-> "OE2" Residue "B GLU 37": "OE1" <-> "OE2" Residue "B GLU 81": "OE1" <-> "OE2" Residue "B GLU 87": "OE1" <-> "OE2" Residue "B GLU 143": "OE1" <-> "OE2" Residue "B ARG 147": "NH1" <-> "NH2" Residue "B GLU 213": "OE1" <-> "OE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 2.77, per 1000 atoms: 0.69 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.77 Conformation dependent library (CDL) restraints added in 750.9 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... running ksdssp... Secondary structure from input PDB file: 14 helices and 3 sheets defined 35.3% alpha, 4.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.72 Creating SS restraints... Processing helix chain 'A' and resid 77 through 93 Proline residue: A 87 - end of helix Processing helix chain 'A' and resid 107 through 128 Processing helix chain 'A' and resid 215 through 242 Processing helix chain 'A' and resid 251 through 263 Processing helix chain 'A' and resid 265 through 280 removed outlier: 4.124A pdb=" N ASN A 280 " --> pdb=" O PHE A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 284 through 290 Processing helix chain 'A' and resid 314 through 322 Processing helix chain 'B' and resid 46 through 48 No H-bonds generated for 'chain 'B' and resid 46 through 48' Processing helix chain 'B' and resid 66 through 69 No H-bonds generated for 'chain 'B' and resid 66 through 69' Processing helix chain 'B' and resid 131 through 134 Processing helix chain 'B' and resid 138 through 156 Processing helix chain 'B' and resid 162 through 173 Processing helix chain 'B' and resid 189 through 205 removed outlier: 3.862A pdb=" N GLN B 192 " --> pdb=" O PRO B 189 " (cutoff:3.500A) removed outlier: 5.144A pdb=" N GLU B 193 " --> pdb=" O VAL B 190 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N SER B 194 " --> pdb=" O PHE B 191 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N LEU B 195 " --> pdb=" O GLN B 192 " (cutoff:3.500A) Processing helix chain 'B' and resid 210 through 214 removed outlier: 3.643A pdb=" N ARG B 214 " --> pdb=" O LEU B 210 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 210 through 214' Processing sheet with id= A, first strand: chain 'A' and resid 158 through 160 Processing sheet with id= B, 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= C, first strand: chain 'B' and resid 70 through 75 129 hydrogen bonds defined for protein. 342 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: 0.88 Time building geometry restraints manager: 1.90 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: 100.06 - 106.85: 156 106.85 - 113.63: 2236 113.63 - 120.42: 1617 120.42 - 127.21: 1517 127.21 - 133.99: 69 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: 3949 3.26 - 3.81: 6309 3.81 - 4.35: 7332 4.35 - 4.90: 13145 Nonbonded interactions: 30921 Sorted by model distance: nonbonded pdb=" O SER B 224 " pdb=" OG SER B 224 " model vdw 2.164 2.440 nonbonded pdb=" OH TYR B 59 " pdb=" OD2 ASP B 230 " model vdw 2.203 2.440 nonbonded pdb=" O TYR B 135 " pdb=" NH1 ARG B 214 " model vdw 2.203 2.520 nonbonded pdb=" O ALA A 83 " pdb=" OH TYR A 259 " model vdw 2.211 2.440 nonbonded pdb=" OE2 GLU B 155 " pdb=" OG SER B 194 " model vdw 2.238 2.440 ... (remaining 30916 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== 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: 0.350 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 1.720 Check model and map are aligned: 0.090 Set scattering table: 0.060 Process input model: 16.730 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.820 ------------------------------------------------------------------------------- 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= 0.455 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 fitting. rotamer outliers: 17 poor density : 68 time to evaluate : 0.530 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: 0.1895 time to fit residues: 19.5608 Evaluate side-chains 70 residues out of total 438 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 58 time to evaluate : 0.465 ------------------------------------------------------------------------------- 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: 2.9990 chunk 37 optimal weight: 8.9990 chunk 20 optimal weight: 0.5980 chunk 12 optimal weight: 0.9990 chunk 25 optimal weight: 1.9990 chunk 19 optimal weight: 0.8980 chunk 38 optimal weight: 0.6980 chunk 14 optimal weight: 0.6980 chunk 23 optimal weight: 0.9980 chunk 28 optimal weight: 0.9990 chunk 44 optimal weight: 10.0000 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7879 moved from start: 0.1133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 4121 Z= 0.189 Angle : 0.511 6.297 5595 Z= 0.263 Chirality : 0.041 0.141 606 Planarity : 0.004 0.035 713 Dihedral : 6.971 59.979 575 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 3.88 % Allowed : 26.03 % Favored : 70.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.36 (0.36), residues: 494 helix: 0.42 (0.37), residues: 180 sheet: -1.36 (0.76), residues: 34 loop : -1.81 (0.36), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 178 HIS 0.003 0.001 HIS B 212 PHE 0.009 0.001 PHE B 231 TYR 0.014 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 88 residues out of total 438 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 71 time to evaluate : 0.482 Fit side-chains REVERT: A 88 MET cc_start: 0.7379 (tmm) cc_final: 0.7165 (tmm) REVERT: A 153 GLU cc_start: 0.8200 (mp0) cc_final: 0.7899 (mp0) REVERT: A 291 ILE cc_start: 0.6091 (OUTLIER) cc_final: 0.5819 (tt) REVERT: B 116 ARG cc_start: 0.7707 (mtm-85) cc_final: 0.7491 (mmm-85) REVERT: B 198 GLU cc_start: 0.8714 (tm-30) cc_final: 0.8420 (tm-30) REVERT: B 222 ARG cc_start: 0.8412 (tmt170) cc_final: 0.8167 (tmt170) outliers start: 17 outliers final: 8 residues processed: 84 average time/residue: 0.1561 time to fit residues: 16.4229 Evaluate side-chains 72 residues out of total 438 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 63 time to evaluate : 0.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 ILE Chi-restraints excluded: chain A residue 172 ILE Chi-restraints excluded: chain A residue 291 ILE Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain B residue 25 GLU Chi-restraints excluded: chain B residue 104 VAL Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain B residue 228 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 24 optimal weight: 0.9980 chunk 13 optimal weight: 2.9990 chunk 37 optimal weight: 7.9990 chunk 30 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 chunk 44 optimal weight: 7.9990 chunk 48 optimal weight: 3.9990 chunk 39 optimal weight: 5.9990 chunk 15 optimal weight: 1.9990 chunk 35 optimal weight: 4.9990 chunk 33 optimal weight: 3.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7959 moved from start: 0.1317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.076 4121 Z= 0.435 Angle : 0.634 7.499 5595 Z= 0.318 Chirality : 0.046 0.134 606 Planarity : 0.005 0.038 713 Dihedral : 6.123 58.667 563 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.29 % Favored : 92.71 % Rotamer: Outliers : 6.39 % Allowed : 25.11 % Favored : 68.49 % 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: -1.33 (0.37), residues: 494 helix: 0.41 (0.38), residues: 182 sheet: -1.55 (0.68), residues: 44 loop : -1.74 (0.38), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 178 HIS 0.005 0.001 HIS B 212 PHE 0.015 0.002 PHE A 218 TYR 0.010 0.002 TYR B 200 ARG 0.003 0.000 ARG A 126 *********************** 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 90 residues out of total 438 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 62 time to evaluate : 0.468 Fit side-chains REVERT: A 76 LEU cc_start: 0.9135 (OUTLIER) cc_final: 0.8756 (tt) REVERT: A 88 MET cc_start: 0.7305 (tmm) cc_final: 0.7061 (tmm) REVERT: A 291 ILE cc_start: 0.6085 (OUTLIER) cc_final: 0.5715 (tt) REVERT: B 116 ARG cc_start: 0.7902 (mtm-85) cc_final: 0.7504 (mmm-85) REVERT: B 205 ASN cc_start: 0.7928 (m-40) cc_final: 0.7626 (m-40) REVERT: B 218 LEU cc_start: 0.8949 (OUTLIER) cc_final: 0.8634 (tt) outliers start: 28 outliers final: 15 residues processed: 84 average time/residue: 0.1484 time to fit residues: 15.8484 Evaluate side-chains 78 residues out of total 438 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 60 time to evaluate : 0.469 ------------------------------------------------------------------------------- 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 111 ILE Chi-restraints excluded: chain A residue 130 SER Chi-restraints excluded: chain A residue 166 ILE 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 30 PHE Chi-restraints excluded: chain B residue 33 ASP 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 218 LEU Chi-restraints excluded: chain B residue 228 SER Chi-restraints excluded: chain B residue 232 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 23 optimal weight: 0.0470 chunk 4 optimal weight: 0.5980 chunk 21 optimal weight: 1.9990 chunk 29 optimal weight: 9.9990 chunk 44 optimal weight: 0.0060 chunk 47 optimal weight: 0.2980 chunk 42 optimal weight: 1.9990 chunk 12 optimal weight: 0.9990 chunk 39 optimal weight: 4.9990 chunk 26 optimal weight: 0.3980 chunk 0 optimal weight: 1.9990 overall best weight: 0.2694 ------------------------------------------------------------------------------- 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 ** B 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7839 moved from start: 0.1837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 4121 Z= 0.130 Angle : 0.514 6.272 5595 Z= 0.256 Chirality : 0.040 0.135 606 Planarity : 0.004 0.031 713 Dihedral : 4.755 34.876 561 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 3.20 % Allowed : 27.17 % 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: -0.65 (0.38), residues: 494 helix: 0.99 (0.39), residues: 182 sheet: -0.84 (0.76), residues: 34 loop : -1.40 (0.37), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 100 HIS 0.003 0.001 HIS B 212 PHE 0.009 0.001 PHE A 287 TYR 0.009 0.001 TYR B 59 ARG 0.001 0.000 ARG A 248 *********************** 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 81 residues out of total 438 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 67 time to evaluate : 0.473 Fit side-chains REVERT: A 88 MET cc_start: 0.7212 (tmm) cc_final: 0.6971 (tmm) REVERT: A 153 GLU cc_start: 0.8168 (mp0) cc_final: 0.7818 (mp0) REVERT: B 94 GLN cc_start: 0.8703 (mt0) cc_final: 0.8446 (tt0) REVERT: B 116 ARG cc_start: 0.7875 (mtm-85) cc_final: 0.7602 (mmm-85) REVERT: B 205 ASN cc_start: 0.8004 (m-40) cc_final: 0.7670 (m-40) outliers start: 14 outliers final: 10 residues processed: 77 average time/residue: 0.1583 time to fit residues: 15.4024 Evaluate side-chains 73 residues out of total 438 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 63 time to evaluate : 0.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 258 CYS 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 129 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 35 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 chunk 40 optimal weight: 0.9980 chunk 32 optimal weight: 4.9990 chunk 0 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 chunk 11 optimal weight: 3.9990 chunk 15 optimal weight: 0.9990 chunk 9 optimal weight: 0.2980 chunk 27 optimal weight: 0.9990 overall best weight: 1.0586 ------------------------------------------------------------------------------- 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 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.1842 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= 0.230 Angle : 0.533 7.918 5595 Z= 0.263 Chirality : 0.041 0.137 606 Planarity : 0.004 0.030 713 Dihedral : 4.745 32.614 561 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % Rotamer: Outliers : 5.02 % Allowed : 26.26 % Favored : 68.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.59 (0.38), residues: 494 helix: 1.11 (0.40), residues: 182 sheet: -1.20 (0.65), residues: 44 loop : -1.35 (0.38), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 178 HIS 0.003 0.001 HIS B 212 PHE 0.010 0.001 PHE A 218 TYR 0.011 0.001 TYR B 200 ARG 0.002 0.000 ARG A 126 *********************** 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 fitting. rotamer outliers: 22 poor density : 62 time to evaluate : 0.432 Fit side-chains REVERT: A 88 MET cc_start: 0.7142 (tmm) cc_final: 0.6867 (tmm) REVERT: A 291 ILE cc_start: 0.6102 (OUTLIER) cc_final: 0.5770 (tt) REVERT: B 66 GLU cc_start: 0.8397 (pm20) cc_final: 0.7874 (pm20) REVERT: B 94 GLN cc_start: 0.8729 (mt0) cc_final: 0.8461 (tt0) REVERT: B 116 ARG cc_start: 0.7958 (mtm-85) cc_final: 0.7747 (mmm-85) REVERT: B 205 ASN cc_start: 0.8148 (m-40) cc_final: 0.7871 (m-40) outliers start: 22 outliers final: 18 residues processed: 78 average time/residue: 0.1269 time to fit residues: 13.0478 Evaluate side-chains 80 residues out of total 438 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 61 time to evaluate : 0.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 125 ILE Chi-restraints excluded: chain A residue 145 ARG Chi-restraints excluded: chain A residue 166 ILE Chi-restraints excluded: chain A residue 172 ILE Chi-restraints excluded: chain A residue 291 ILE Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 348 SER 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 127 SER Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 156 GLU Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 232 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 11 optimal weight: 2.9990 chunk 47 optimal weight: 2.9990 chunk 39 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 3 optimal weight: 0.8980 chunk 15 optimal weight: 0.9990 chunk 24 optimal weight: 0.0270 chunk 45 optimal weight: 1.9990 chunk 5 optimal weight: 0.8980 chunk 27 optimal weight: 5.9990 chunk 34 optimal weight: 0.7980 overall best weight: 0.7240 ------------------------------------------------------------------------------- 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 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 moved from start: 0.2041 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= 0.175 Angle : 0.507 7.151 5595 Z= 0.251 Chirality : 0.041 0.137 606 Planarity : 0.004 0.030 713 Dihedral : 4.568 33.889 561 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 5.48 % Allowed : 26.03 % Favored : 68.49 % 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 (0.38), residues: 494 helix: 1.30 (0.40), residues: 181 sheet: -0.70 (0.75), residues: 34 loop : -1.25 (0.37), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 100 HIS 0.005 0.001 HIS B 212 PHE 0.009 0.001 PHE A 287 TYR 0.013 0.001 TYR B 200 ARG 0.001 0.000 ARG A 126 *********************** 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 fitting. rotamer outliers: 24 poor density : 62 time to evaluate : 0.463 Fit side-chains REVERT: A 76 LEU cc_start: 0.9043 (OUTLIER) cc_final: 0.8723 (tt) REVERT: A 88 MET cc_start: 0.7136 (tmm) cc_final: 0.6855 (tmm) REVERT: A 103 GLN cc_start: 0.6688 (mp10) cc_final: 0.6373 (mm-40) REVERT: B 66 GLU cc_start: 0.8282 (pm20) cc_final: 0.8027 (pm20) REVERT: B 94 GLN cc_start: 0.8722 (mt0) cc_final: 0.8458 (tt0) REVERT: B 116 ARG cc_start: 0.8037 (mtm-85) cc_final: 0.7836 (mmm-85) outliers start: 24 outliers final: 16 residues processed: 78 average time/residue: 0.1286 time to fit residues: 13.2983 Evaluate side-chains 80 residues out of total 438 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 63 time to evaluate : 0.465 ------------------------------------------------------------------------------- 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 125 ILE Chi-restraints excluded: chain A residue 145 ARG 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 348 SER 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 123 VAL Chi-restraints excluded: chain B residue 127 SER Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 232 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 26 optimal weight: 5.9990 chunk 39 optimal weight: 1.9990 chunk 47 optimal weight: 0.4980 chunk 29 optimal weight: 20.0000 chunk 28 optimal weight: 4.9990 chunk 21 optimal weight: 0.9990 chunk 18 optimal weight: 0.0980 chunk 14 optimal weight: 0.9980 chunk 9 optimal weight: 3.9990 chunk 30 optimal weight: 3.9990 chunk 32 optimal weight: 4.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- 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 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7878 moved from start: 0.2076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4121 Z= 0.210 Angle : 0.538 7.043 5595 Z= 0.266 Chirality : 0.041 0.140 606 Planarity : 0.004 0.031 713 Dihedral : 4.385 33.527 559 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 3.65 % Allowed : 27.17 % Favored : 69.18 % 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: -0.37 (0.38), residues: 494 helix: 1.15 (0.38), residues: 190 sheet: -0.63 (0.75), residues: 34 loop : -1.25 (0.39), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 178 HIS 0.008 0.001 HIS B 212 PHE 0.009 0.001 PHE A 287 TYR 0.007 0.001 TYR B 117 ARG 0.001 0.000 ARG A 126 *********************** 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 fitting. rotamer outliers: 16 poor density : 63 time to evaluate : 0.458 Fit side-chains REVERT: A 76 LEU cc_start: 0.9057 (OUTLIER) cc_final: 0.8721 (tt) REVERT: A 88 MET cc_start: 0.7111 (tmm) cc_final: 0.6816 (tmm) REVERT: A 103 GLN cc_start: 0.6756 (mp10) cc_final: 0.6522 (mm-40) REVERT: B 66 GLU cc_start: 0.8235 (pm20) cc_final: 0.7979 (pm20) REVERT: B 94 GLN cc_start: 0.8727 (mt0) cc_final: 0.8465 (tt0) outliers start: 16 outliers final: 12 residues processed: 75 average time/residue: 0.1416 time to fit residues: 13.8785 Evaluate side-chains 76 residues out of total 438 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 63 time to evaluate : 0.472 ------------------------------------------------------------------------------- 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 125 ILE Chi-restraints excluded: chain A residue 166 ILE Chi-restraints excluded: chain A residue 172 ILE 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 109 THR Chi-restraints excluded: chain B residue 127 SER Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 232 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 23 optimal weight: 4.9990 chunk 4 optimal weight: 0.9990 chunk 37 optimal weight: 0.8980 chunk 42 optimal weight: 0.6980 chunk 45 optimal weight: 0.9980 chunk 41 optimal weight: 0.0170 chunk 44 optimal weight: 0.0060 chunk 26 optimal weight: 4.9990 chunk 19 optimal weight: 0.9980 chunk 34 optimal weight: 0.2980 chunk 13 optimal weight: 0.4980 overall best weight: 0.3034 ------------------------------------------------------------------------------- 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 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7812 moved from start: 0.2469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 4121 Z= 0.123 Angle : 0.495 7.077 5595 Z= 0.245 Chirality : 0.040 0.132 606 Planarity : 0.004 0.031 713 Dihedral : 4.050 31.654 559 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 2.05 % Allowed : 29.22 % Favored : 68.72 % 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 (0.39), residues: 494 helix: 1.48 (0.39), residues: 188 sheet: -0.51 (0.76), residues: 34 loop : -1.10 (0.39), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 100 HIS 0.007 0.001 HIS B 212 PHE 0.009 0.001 PHE A 287 TYR 0.007 0.001 TYR A 115 ARG 0.004 0.000 ARG B 116 *********************** 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 72 residues out of total 438 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 63 time to evaluate : 0.416 Fit side-chains REVERT: A 88 MET cc_start: 0.7096 (tmm) cc_final: 0.6825 (tmm) REVERT: A 153 GLU cc_start: 0.8147 (mp0) cc_final: 0.7808 (mp0) REVERT: B 66 GLU cc_start: 0.8184 (pm20) cc_final: 0.7942 (pm20) REVERT: B 94 GLN cc_start: 0.8716 (mt0) cc_final: 0.8456 (tt0) REVERT: B 116 ARG cc_start: 0.8384 (mmm-85) cc_final: 0.8123 (tpp80) outliers start: 9 outliers final: 6 residues processed: 69 average time/residue: 0.1498 time to fit residues: 13.4551 Evaluate side-chains 68 residues out of total 438 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 62 time to evaluate : 0.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 VAL 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 170 LEU Chi-restraints excluded: chain B residue 232 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 39 optimal weight: 2.9990 chunk 41 optimal weight: 0.0570 chunk 43 optimal weight: 0.8980 chunk 28 optimal weight: 3.9990 chunk 46 optimal weight: 0.0070 chunk 22 optimal weight: 0.0670 chunk 32 optimal weight: 0.6980 chunk 48 optimal weight: 0.8980 chunk 44 optimal weight: 1.9990 chunk 38 optimal weight: 4.9990 chunk 4 optimal weight: 0.5980 overall best weight: 0.2854 ------------------------------------------------------------------------------- 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 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7807 moved from start: 0.2596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 4121 Z= 0.129 Angle : 0.523 9.365 5595 Z= 0.249 Chirality : 0.040 0.135 606 Planarity : 0.004 0.032 713 Dihedral : 3.884 29.285 559 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 2.05 % Allowed : 28.77 % Favored : 69.18 % 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: 0.09 (0.39), residues: 494 helix: 1.65 (0.39), residues: 188 sheet: -0.41 (0.77), residues: 34 loop : -1.06 (0.39), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 100 HIS 0.007 0.001 HIS B 212 PHE 0.010 0.001 PHE A 287 TYR 0.007 0.001 TYR B 117 ARG 0.005 0.000 ARG B 116 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 988 Ramachandran restraints generated. 494 Oldfield, 0 Emsley, 494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 988 Ramachandran restraints generated. 494 Oldfield, 0 Emsley, 494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 438 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 64 time to evaluate : 0.442 Fit side-chains REVERT: A 88 MET cc_start: 0.7092 (tmm) cc_final: 0.6817 (tmm) REVERT: A 153 GLU cc_start: 0.8121 (mp0) cc_final: 0.7822 (mp0) REVERT: B 66 GLU cc_start: 0.8171 (pm20) cc_final: 0.7947 (pm20) REVERT: B 94 GLN cc_start: 0.8707 (mt0) cc_final: 0.8451 (tt0) REVERT: B 116 ARG cc_start: 0.8344 (mmm-85) cc_final: 0.8113 (tpp80) outliers start: 9 outliers final: 8 residues processed: 70 average time/residue: 0.1420 time to fit residues: 12.8487 Evaluate side-chains 69 residues out of total 438 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 61 time to evaluate : 0.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 318 MET 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 123 VAL Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 232 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 30 optimal weight: 5.9990 chunk 23 optimal weight: 0.1980 chunk 41 optimal weight: 0.4980 chunk 11 optimal weight: 0.9980 chunk 35 optimal weight: 0.6980 chunk 5 optimal weight: 0.2980 chunk 10 optimal weight: 0.7980 chunk 38 optimal weight: 0.6980 chunk 16 optimal weight: 0.9990 chunk 39 optimal weight: 3.9990 chunk 4 optimal weight: 0.5980 overall best weight: 0.4580 ------------------------------------------------------------------------------- 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 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7821 moved from start: 0.2691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 4121 Z= 0.140 Angle : 0.524 9.226 5595 Z= 0.249 Chirality : 0.041 0.198 606 Planarity : 0.004 0.032 713 Dihedral : 3.857 28.011 559 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 2.28 % Allowed : 28.77 % Favored : 68.95 % 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: 0.09 (0.39), residues: 494 helix: 1.61 (0.39), residues: 189 sheet: -0.43 (0.75), residues: 34 loop : -1.04 (0.39), residues: 271 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 100 HIS 0.006 0.001 HIS B 212 PHE 0.008 0.001 PHE B 231 TYR 0.006 0.001 TYR A 115 ARG 0.004 0.000 ARG B 116 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 988 Ramachandran restraints generated. 494 Oldfield, 0 Emsley, 494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 988 Ramachandran restraints generated. 494 Oldfield, 0 Emsley, 494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 438 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 65 time to evaluate : 0.500 Fit side-chains REVERT: A 88 MET cc_start: 0.7089 (tmm) cc_final: 0.6823 (tmm) REVERT: A 153 GLU cc_start: 0.8108 (mp0) cc_final: 0.7805 (mp0) REVERT: B 66 GLU cc_start: 0.8138 (pm20) cc_final: 0.7902 (pm20) REVERT: B 116 ARG cc_start: 0.8320 (mmm-85) cc_final: 0.8088 (tpp80) outliers start: 10 outliers final: 10 residues processed: 72 average time/residue: 0.1466 time to fit residues: 13.7306 Evaluate side-chains 72 residues out of total 438 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 62 time to evaluate : 0.465 ------------------------------------------------------------------------------- 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 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 112 VAL Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 232 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 7 optimal weight: 0.0070 chunk 34 optimal weight: 3.9990 chunk 2 optimal weight: 0.4980 chunk 28 optimal weight: 3.9990 chunk 44 optimal weight: 0.0060 chunk 26 optimal weight: 0.0670 chunk 33 optimal weight: 0.8980 chunk 1 optimal weight: 0.9980 chunk 31 optimal weight: 0.7980 chunk 29 optimal weight: 6.9990 chunk 19 optimal weight: 0.8980 overall best weight: 0.2752 ------------------------------------------------------------------------------- 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 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 205 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.177509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.132891 restraints weight = 4660.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.134047 restraints weight = 4094.221| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.134478 restraints weight = 3433.967| |-----------------------------------------------------------------------------| r_work (final): 0.3188 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7695 moved from start: 0.2829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 4121 Z= 0.128 Angle : 0.520 9.521 5595 Z= 0.246 Chirality : 0.040 0.181 606 Planarity : 0.004 0.032 713 Dihedral : 3.717 26.072 559 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 2.51 % Allowed : 28.31 % Favored : 69.18 % 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: 0.18 (0.39), residues: 494 helix: 1.73 (0.39), residues: 188 sheet: -0.36 (0.76), residues: 34 loop : -1.01 (0.39), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 100 HIS 0.006 0.001 HIS B 212 PHE 0.020 0.001 PHE A 287 TYR 0.007 0.001 TYR B 200 ARG 0.004 0.000 ARG B 116 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1237.38 seconds wall clock time: 22 minutes 54.64 seconds (1374.64 seconds total)