Starting phenix.real_space_refine on Mon Sep 23 18:27:20 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ieb_35377/09_2024/8ieb_35377.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ieb_35377/09_2024/8ieb_35377.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.03 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ieb_35377/09_2024/8ieb_35377.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ieb_35377/09_2024/8ieb_35377.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ieb_35377/09_2024/8ieb_35377.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ieb_35377/09_2024/8ieb_35377.cif" } resolution = 3.03 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.012 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 2 5.49 5 S 35 5.16 5 C 2934 2.51 5 N 691 2.21 5 O 754 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 4416 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2062 Number of conformers: 1 Conformer: "" Number of residues, atoms: 269, 2062 Classifications: {'peptide': 269} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 9, 'TRANS': 259} Chain breaks: 2 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "B" Number of atoms: 2250 Number of conformers: 1 Conformer: "" Number of residues, atoms: 289, 2250 Classifications: {'peptide': 289} Link IDs: {'PTRANS': 10, 'TRANS': 278} Chain breaks: 1 Chain: "A" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 52 Unusual residues: {'PC1': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Chain: "B" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 52 Unusual residues: {'PC1': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Time building chain proxies: 4.42, per 1000 atoms: 1.00 Number of scatterers: 4416 At special positions: 0 Unit cell: (86.67, 87.48, 90.72, 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) S 35 16.00 P 2 15.00 O 754 8.00 N 691 7.00 C 2934 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 191 " - pdb=" SG CYS A 216 " distance=2.03 Simple disulfide: pdb=" SG CYS B 191 " - pdb=" SG CYS B 216 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.14 Conformation dependent library (CDL) restraints added in 534.9 milliseconds 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1040 Finding SS restraints... Secondary structure from input PDB file: 19 helices and 1 sheets defined 76.2% alpha, 7.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.65 Creating SS restraints... Processing helix chain 'A' and resid 46 through 74 Processing helix chain 'A' and resid 77 through 82 Processing helix chain 'A' and resid 84 through 105 removed outlier: 3.540A pdb=" N ASN A 88 " --> pdb=" O SER A 84 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ILE A 89 " --> pdb=" O PRO A 85 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N VAL A 90 " --> pdb=" O ASN A 86 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N THR A 91 " --> pdb=" O LEU A 87 " (cutoff:3.500A) Processing helix chain 'A' and resid 115 through 151 Proline residue: A 137 - end of helix Processing helix chain 'A' and resid 161 through 187 removed outlier: 3.645A pdb=" N LEU A 165 " --> pdb=" O LYS A 161 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N TRP A 183 " --> pdb=" O LEU A 179 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ASP A 187 " --> pdb=" O TRP A 183 " (cutoff:3.500A) Processing helix chain 'A' and resid 220 through 246 removed outlier: 3.848A pdb=" N TRP A 224 " --> pdb=" O TYR A 220 " (cutoff:3.500A) Processing helix chain 'A' and resid 257 through 280 Processing helix chain 'A' and resid 284 through 317 Proline residue: A 310 - end of helix removed outlier: 3.660A pdb=" N ALA A 317 " --> pdb=" O LYS A 313 " (cutoff:3.500A) Processing helix chain 'B' and resid 46 through 74 Processing helix chain 'B' and resid 77 through 83 Processing helix chain 'B' and resid 84 through 105 removed outlier: 3.543A pdb=" N VAL B 90 " --> pdb=" O ASN B 86 " (cutoff:3.500A) Processing helix chain 'B' and resid 116 through 150 removed outlier: 3.870A pdb=" N MET B 126 " --> pdb=" O THR B 122 " (cutoff:3.500A) Proline residue: B 137 - end of helix Processing helix chain 'B' and resid 161 through 187 removed outlier: 3.755A pdb=" N LEU B 165 " --> pdb=" O LYS B 161 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ASP B 187 " --> pdb=" O TRP B 183 " (cutoff:3.500A) Processing helix chain 'B' and resid 220 through 246 removed outlier: 3.535A pdb=" N TRP B 224 " --> pdb=" O TYR B 220 " (cutoff:3.500A) Processing helix chain 'B' and resid 256 through 281 Processing helix chain 'B' and resid 284 through 315 Proline residue: B 310 - end of helix Processing helix chain 'B' and resid 316 through 319 Processing helix chain 'B' and resid 324 through 328 removed outlier: 3.552A pdb=" N ARG B 327 " --> pdb=" O THR B 324 " (cutoff:3.500A) Processing helix chain 'B' and resid 329 through 333 Processing sheet with id=AA1, first strand: chain 'A' and resid 206 through 216 removed outlier: 4.040A pdb=" N PHE A 215 " --> pdb=" O LEU A 192 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N LEU A 192 " --> pdb=" O PHE A 215 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N LEU A 195 " --> pdb=" O MET B 199 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N LEU B 195 " --> pdb=" O MET A 199 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N VAL A 201 " --> pdb=" O GLN B 193 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLN B 193 " --> pdb=" O VAL A 201 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N GLN B 190 " --> pdb=" O ALA B 217 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N PHE B 215 " --> pdb=" O LEU B 192 " (cutoff:3.500A) 349 hydrogen bonds defined for protein. 1035 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.68 Time building geometry restraints manager: 1.31 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 631 1.32 - 1.44: 1203 1.44 - 1.57: 2620 1.57 - 1.70: 4 1.70 - 1.83: 50 Bond restraints: 4508 Sorted by residual: bond pdb=" C39 PC1 A 601 " pdb=" C3A PC1 A 601 " ideal model delta sigma weight residual 1.524 1.318 0.206 2.00e-02 2.50e+03 1.06e+02 bond pdb=" C39 PC1 B 601 " pdb=" C3A PC1 B 601 " ideal model delta sigma weight residual 1.524 1.320 0.204 2.00e-02 2.50e+03 1.04e+02 bond pdb=" C31 PC1 B 601 " pdb=" O31 PC1 B 601 " ideal model delta sigma weight residual 1.330 1.426 -0.096 2.00e-02 2.50e+03 2.30e+01 bond pdb=" C31 PC1 A 601 " pdb=" O31 PC1 A 601 " ideal model delta sigma weight residual 1.330 1.418 -0.088 2.00e-02 2.50e+03 1.95e+01 bond pdb=" C2 PC1 B 601 " pdb=" O21 PC1 B 601 " ideal model delta sigma weight residual 1.430 1.380 0.050 2.00e-02 2.50e+03 6.19e+00 ... (remaining 4503 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.98: 6016 2.98 - 5.95: 81 5.95 - 8.93: 21 8.93 - 11.91: 1 11.91 - 14.89: 2 Bond angle restraints: 6121 Sorted by residual: angle pdb=" O12 PC1 B 601 " pdb=" P PC1 B 601 " pdb=" O14 PC1 B 601 " ideal model delta sigma weight residual 123.67 108.78 14.89 3.00e+00 1.11e-01 2.46e+01 angle pdb=" O12 PC1 A 601 " pdb=" P PC1 A 601 " pdb=" O14 PC1 A 601 " ideal model delta sigma weight residual 123.67 109.52 14.15 3.00e+00 1.11e-01 2.22e+01 angle pdb=" N PRO A 252 " pdb=" CA PRO A 252 " pdb=" C PRO A 252 " ideal model delta sigma weight residual 110.70 114.71 -4.01 1.22e+00 6.72e-01 1.08e+01 angle pdb=" C ASP A 109 " pdb=" N VAL A 110 " pdb=" CA VAL A 110 " ideal model delta sigma weight residual 121.70 127.56 -5.86 1.80e+00 3.09e-01 1.06e+01 angle pdb=" N PRO B 252 " pdb=" CA PRO B 252 " pdb=" C PRO B 252 " ideal model delta sigma weight residual 110.70 114.66 -3.96 1.22e+00 6.72e-01 1.05e+01 ... (remaining 6116 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.13: 2358 17.13 - 34.27: 238 34.27 - 51.40: 51 51.40 - 68.54: 16 68.54 - 85.67: 7 Dihedral angle restraints: 2670 sinusoidal: 1062 harmonic: 1608 Sorted by residual: dihedral pdb=" CA ILE B 307 " pdb=" C ILE B 307 " pdb=" N PHE B 308 " pdb=" CA PHE B 308 " ideal model delta harmonic sigma weight residual 180.00 -160.91 -19.09 0 5.00e+00 4.00e-02 1.46e+01 dihedral pdb=" CA MET B 82 " pdb=" C MET B 82 " pdb=" N SER B 83 " pdb=" CA SER B 83 " ideal model delta harmonic sigma weight residual 180.00 161.58 18.42 0 5.00e+00 4.00e-02 1.36e+01 dihedral pdb=" CA ILE A 307 " pdb=" C ILE A 307 " pdb=" N PHE A 308 " pdb=" CA PHE A 308 " ideal model delta harmonic sigma weight residual 180.00 -163.98 -16.02 0 5.00e+00 4.00e-02 1.03e+01 ... (remaining 2667 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 575 0.051 - 0.102: 141 0.102 - 0.152: 37 0.152 - 0.203: 2 0.203 - 0.254: 2 Chirality restraints: 757 Sorted by residual: chirality pdb=" CB ILE A 189 " pdb=" CA ILE A 189 " pdb=" CG1 ILE A 189 " pdb=" CG2 ILE A 189 " both_signs ideal model delta sigma weight residual False 2.64 2.39 0.25 2.00e-01 2.50e+01 1.61e+00 chirality pdb=" CG LEU A 92 " pdb=" CB LEU A 92 " pdb=" CD1 LEU A 92 " pdb=" CD2 LEU A 92 " both_signs ideal model delta sigma weight residual False -2.59 -2.36 -0.23 2.00e-01 2.50e+01 1.27e+00 chirality pdb=" CB ILE A 260 " pdb=" CA ILE A 260 " pdb=" CG1 ILE A 260 " pdb=" CG2 ILE A 260 " both_signs ideal model delta sigma weight residual False 2.64 2.45 0.19 2.00e-01 2.50e+01 9.37e-01 ... (remaining 754 not shown) Planarity restraints: 709 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO B 252 " -0.046 5.00e-02 4.00e+02 6.92e-02 7.66e+00 pdb=" N PRO B 253 " 0.120 5.00e-02 4.00e+02 pdb=" CA PRO B 253 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO B 253 " -0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO A 252 " -0.044 5.00e-02 4.00e+02 6.50e-02 6.76e+00 pdb=" N PRO A 253 " 0.112 5.00e-02 4.00e+02 pdb=" CA PRO A 253 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO A 253 " -0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER A 251 " 0.032 5.00e-02 4.00e+02 4.78e-02 3.66e+00 pdb=" N PRO A 252 " -0.083 5.00e-02 4.00e+02 pdb=" CA PRO A 252 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 252 " 0.026 5.00e-02 4.00e+02 ... (remaining 706 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 336 2.74 - 3.28: 4383 3.28 - 3.82: 7448 3.82 - 4.36: 8174 4.36 - 4.90: 14626 Nonbonded interactions: 34967 Sorted by model distance: nonbonded pdb=" O VAL A 298 " pdb=" OG1 THR A 302 " model vdw 2.198 3.040 nonbonded pdb=" O TYR B 146 " pdb=" OG1 THR B 150 " model vdw 2.254 3.040 nonbonded pdb=" O THR A 182 " pdb=" OG1 THR A 186 " model vdw 2.271 3.040 nonbonded pdb=" O LEU B 274 " pdb=" OG1 THR B 278 " model vdw 2.295 3.040 nonbonded pdb=" O SER A 114 " pdb=" OG SER A 114 " model vdw 2.331 3.040 ... (remaining 34962 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 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 44 through 110 or resid 115 through 318 or resid 601)) selection = (chain 'B' and (resid 44 through 110 or resid 115 through 150 or (resid 151 thro \ ugh 152 and (name N or name CA or name C or name O or name CB )) or resid 153 th \ rough 154 or (resid 155 and (name N or name CA or name C or name O or name CB )) \ or resid 159 through 318 or resid 601)) } 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 individual isotropic 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: 5.760 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: 0.200 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 16.550 Find NCS groups from input model: 0.170 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:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7586 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 0.206 4508 Z= 0.515 Angle : 0.909 14.886 6121 Z= 0.418 Chirality : 0.049 0.254 757 Planarity : 0.007 0.069 709 Dihedral : 15.358 85.674 1624 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 0.00 % Allowed : 0.41 % Favored : 99.59 % 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: 0.96 (0.34), residues: 548 helix: 1.21 (0.24), residues: 395 sheet: 1.82 (0.99), residues: 36 loop : -1.62 (0.55), residues: 117 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP A 229 HIS 0.002 0.000 HIS A 248 PHE 0.023 0.002 PHE A 306 TYR 0.010 0.002 TYR A 280 ARG 0.004 0.000 ARG B 144 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 495 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 100 time to evaluate : 0.468 Fit side-chains REVERT: A 199 MET cc_start: 0.6402 (ttm) cc_final: 0.6161 (ttm) REVERT: A 215 PHE cc_start: 0.7818 (p90) cc_final: 0.7361 (p90) REVERT: B 82 MET cc_start: 0.7560 (ttt) cc_final: 0.7343 (ttm) REVERT: B 96 CYS cc_start: 0.8471 (p) cc_final: 0.8271 (p) REVERT: B 122 THR cc_start: 0.8140 (t) cc_final: 0.7839 (p) REVERT: B 174 MET cc_start: 0.7415 (ttm) cc_final: 0.6914 (ttm) REVERT: B 215 PHE cc_start: 0.6930 (p90) cc_final: 0.6620 (p90) REVERT: B 216 CYS cc_start: 0.6227 (t) cc_final: 0.6016 (t) REVERT: B 222 ASP cc_start: 0.8256 (m-30) cc_final: 0.8008 (m-30) REVERT: B 261 MET cc_start: 0.8298 (mmm) cc_final: 0.8084 (mmp) outliers start: 0 outliers final: 0 residues processed: 100 average time/residue: 0.1447 time to fit residues: 19.9061 Evaluate side-chains 91 residues out of total 495 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 91 time to evaluate : 0.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 45 optimal weight: 0.2980 chunk 40 optimal weight: 0.9980 chunk 22 optimal weight: 0.5980 chunk 13 optimal weight: 1.9990 chunk 27 optimal weight: 0.7980 chunk 21 optimal weight: 0.0980 chunk 42 optimal weight: 5.9990 chunk 16 optimal weight: 0.8980 chunk 25 optimal weight: 0.0870 chunk 31 optimal weight: 0.2980 chunk 49 optimal weight: 0.0980 overall best weight: 0.1758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 265 ASN B 314 GLN B 322 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7584 moved from start: 0.1074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 4508 Z= 0.188 Angle : 0.563 9.907 6121 Z= 0.292 Chirality : 0.041 0.212 757 Planarity : 0.005 0.042 709 Dihedral : 12.520 75.599 676 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 0.61 % Allowed : 9.55 % Favored : 89.84 % 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: 2.17 (0.36), residues: 548 helix: 2.20 (0.25), residues: 394 sheet: 2.70 (1.07), residues: 28 loop : -1.43 (0.58), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 54 HIS 0.002 0.000 HIS A 248 PHE 0.016 0.001 PHE B 66 TYR 0.008 0.001 TYR A 280 ARG 0.002 0.000 ARG A 144 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 495 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 91 time to evaluate : 0.472 Fit side-chains REVERT: B 122 THR cc_start: 0.8252 (t) cc_final: 0.8017 (p) REVERT: B 174 MET cc_start: 0.7389 (ttm) cc_final: 0.6912 (ttm) REVERT: B 216 CYS cc_start: 0.5525 (t) cc_final: 0.5242 (t) REVERT: B 261 MET cc_start: 0.8338 (mmm) cc_final: 0.8136 (mmp) outliers start: 3 outliers final: 1 residues processed: 93 average time/residue: 0.1142 time to fit residues: 14.7140 Evaluate side-chains 89 residues out of total 495 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 88 time to evaluate : 0.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 322 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 27 optimal weight: 0.9980 chunk 15 optimal weight: 6.9990 chunk 40 optimal weight: 2.9990 chunk 33 optimal weight: 0.8980 chunk 13 optimal weight: 0.0770 chunk 49 optimal weight: 0.3980 chunk 53 optimal weight: 2.9990 chunk 43 optimal weight: 0.7980 chunk 48 optimal weight: 0.2980 chunk 16 optimal weight: 0.2980 chunk 39 optimal weight: 0.5980 overall best weight: 0.3338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 265 ASN B 311 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7606 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 : 0.004 0.029 4508 Z= 0.246 Angle : 0.575 9.060 6121 Z= 0.298 Chirality : 0.043 0.307 757 Planarity : 0.005 0.042 709 Dihedral : 11.962 73.226 676 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 1.02 % Allowed : 13.41 % Favored : 85.57 % 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: 2.41 (0.36), residues: 548 helix: 2.45 (0.25), residues: 393 sheet: 2.49 (1.08), residues: 24 loop : -1.39 (0.57), residues: 131 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A 54 HIS 0.001 0.000 HIS A 248 PHE 0.017 0.001 PHE B 66 TYR 0.013 0.001 TYR A 280 ARG 0.003 0.000 ARG B 78 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 495 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 91 time to evaluate : 0.460 Fit side-chains revert: symmetry clash REVERT: B 174 MET cc_start: 0.7410 (ttm) cc_final: 0.6943 (ttm) REVERT: B 216 CYS cc_start: 0.5642 (t) cc_final: 0.5389 (t) REVERT: B 261 MET cc_start: 0.8371 (mmm) cc_final: 0.8165 (mmp) outliers start: 5 outliers final: 3 residues processed: 93 average time/residue: 0.1141 time to fit residues: 14.7440 Evaluate side-chains 88 residues out of total 495 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 85 time to evaluate : 0.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain B residue 104 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 48 optimal weight: 0.1980 chunk 36 optimal weight: 0.4980 chunk 25 optimal weight: 0.5980 chunk 5 optimal weight: 0.1980 chunk 23 optimal weight: 0.6980 chunk 32 optimal weight: 0.9990 chunk 49 optimal weight: 0.3980 chunk 52 optimal weight: 0.5980 chunk 46 optimal weight: 0.0570 chunk 14 optimal weight: 0.7980 chunk 43 optimal weight: 0.4980 overall best weight: 0.2698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 265 ASN B 322 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7601 moved from start: 0.1524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4508 Z= 0.217 Angle : 0.550 9.394 6121 Z= 0.286 Chirality : 0.043 0.290 757 Planarity : 0.004 0.042 709 Dihedral : 11.450 72.090 676 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 1.83 % Allowed : 14.43 % Favored : 83.74 % 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: 2.47 (0.36), residues: 548 helix: 2.57 (0.24), residues: 393 sheet: 2.75 (1.36), residues: 14 loop : -1.35 (0.56), residues: 141 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP A 54 HIS 0.001 0.000 HIS A 248 PHE 0.015 0.001 PHE B 275 TYR 0.012 0.001 TYR A 280 ARG 0.002 0.000 ARG B 123 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 495 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 91 time to evaluate : 0.450 Fit side-chains revert: symmetry clash REVERT: A 199 MET cc_start: 0.6627 (ttm) cc_final: 0.6320 (ttm) REVERT: B 174 MET cc_start: 0.7401 (ttm) cc_final: 0.6940 (ttm) REVERT: B 187 ASP cc_start: 0.7448 (t0) cc_final: 0.7245 (t0) REVERT: B 216 CYS cc_start: 0.5516 (t) cc_final: 0.5258 (t) REVERT: B 261 MET cc_start: 0.8366 (mmm) cc_final: 0.8160 (mmp) outliers start: 9 outliers final: 6 residues processed: 95 average time/residue: 0.1125 time to fit residues: 14.8630 Evaluate side-chains 95 residues out of total 495 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 89 time to evaluate : 0.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 83 SER Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain B residue 104 LEU Chi-restraints excluded: chain B residue 181 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 29 optimal weight: 0.5980 chunk 0 optimal weight: 1.9990 chunk 38 optimal weight: 0.0980 chunk 21 optimal weight: 0.1980 chunk 44 optimal weight: 0.0670 chunk 36 optimal weight: 0.1980 chunk 26 optimal weight: 0.9990 chunk 46 optimal weight: 0.4980 chunk 13 optimal weight: 0.2980 chunk 17 optimal weight: 0.6980 chunk 47 optimal weight: 0.3980 overall best weight: 0.1718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 214 HIS A 265 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7579 moved from start: 0.1698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 4508 Z= 0.176 Angle : 0.548 9.851 6121 Z= 0.280 Chirality : 0.041 0.300 757 Planarity : 0.004 0.043 709 Dihedral : 11.142 71.828 676 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 2.03 % Allowed : 15.85 % Favored : 82.11 % 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: 2.56 (0.36), residues: 548 helix: 2.64 (0.24), residues: 394 sheet: 2.63 (1.41), residues: 14 loop : -1.33 (0.56), residues: 140 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP A 54 HIS 0.004 0.000 HIS A 214 PHE 0.017 0.001 PHE A 318 TYR 0.010 0.001 TYR A 280 ARG 0.002 0.000 ARG B 123 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 495 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 88 time to evaluate : 0.478 Fit side-chains revert: symmetry clash REVERT: A 199 MET cc_start: 0.6581 (ttm) cc_final: 0.6244 (ttm) REVERT: A 262 VAL cc_start: 0.8168 (p) cc_final: 0.7959 (p) REVERT: B 174 MET cc_start: 0.7391 (ttm) cc_final: 0.6931 (ttm) REVERT: B 187 ASP cc_start: 0.7441 (t0) cc_final: 0.7188 (t0) REVERT: B 216 CYS cc_start: 0.5591 (t) cc_final: 0.5358 (t) REVERT: B 261 MET cc_start: 0.8348 (mmm) cc_final: 0.8136 (mmp) outliers start: 10 outliers final: 6 residues processed: 92 average time/residue: 0.1203 time to fit residues: 15.5267 Evaluate side-chains 93 residues out of total 495 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 87 time to evaluate : 0.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 83 SER Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain B residue 104 LEU Chi-restraints excluded: chain B residue 181 MET Chi-restraints excluded: chain B residue 249 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 10 optimal weight: 0.0870 chunk 30 optimal weight: 0.2980 chunk 12 optimal weight: 0.5980 chunk 52 optimal weight: 0.0870 chunk 43 optimal weight: 0.0980 chunk 24 optimal weight: 0.9980 chunk 4 optimal weight: 0.9990 chunk 17 optimal weight: 0.6980 chunk 27 optimal weight: 0.4980 chunk 50 optimal weight: 0.8980 chunk 5 optimal weight: 0.2980 overall best weight: 0.1736 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 265 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7576 moved from start: 0.1791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4508 Z= 0.173 Angle : 0.558 10.395 6121 Z= 0.282 Chirality : 0.041 0.325 757 Planarity : 0.004 0.044 709 Dihedral : 10.879 71.957 676 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 1.42 % Allowed : 16.87 % Favored : 81.71 % 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: 2.58 (0.36), residues: 548 helix: 2.67 (0.24), residues: 394 sheet: 2.61 (1.46), residues: 14 loop : -1.37 (0.56), residues: 140 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 54 HIS 0.001 0.000 HIS A 248 PHE 0.018 0.001 PHE B 275 TYR 0.012 0.001 TYR A 280 ARG 0.002 0.000 ARG B 123 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 495 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 89 time to evaluate : 0.467 Fit side-chains REVERT: A 199 MET cc_start: 0.6536 (ttm) cc_final: 0.6193 (ttm) REVERT: A 262 VAL cc_start: 0.8170 (p) cc_final: 0.7968 (p) REVERT: B 116 MET cc_start: 0.6675 (tpp) cc_final: 0.6417 (mpp) REVERT: B 125 SER cc_start: 0.8239 (t) cc_final: 0.7909 (p) REVERT: B 174 MET cc_start: 0.7388 (ttm) cc_final: 0.6949 (ttm) REVERT: B 187 ASP cc_start: 0.7474 (t0) cc_final: 0.7246 (t0) REVERT: B 216 CYS cc_start: 0.5604 (t) cc_final: 0.5378 (t) REVERT: B 261 MET cc_start: 0.8334 (mmm) cc_final: 0.8127 (mmp) outliers start: 7 outliers final: 4 residues processed: 93 average time/residue: 0.1160 time to fit residues: 14.9087 Evaluate side-chains 88 residues out of total 495 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 84 time to evaluate : 0.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain B residue 104 LEU Chi-restraints excluded: chain B residue 181 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 29 optimal weight: 0.6980 chunk 38 optimal weight: 0.0980 chunk 43 optimal weight: 0.7980 chunk 52 optimal weight: 0.5980 chunk 32 optimal weight: 0.9980 chunk 31 optimal weight: 0.5980 chunk 24 optimal weight: 0.9990 chunk 20 optimal weight: 0.9980 chunk 15 optimal weight: 3.9990 chunk 10 optimal weight: 0.8980 chunk 33 optimal weight: 0.3980 overall best weight: 0.4780 ------------------------------------------------------------------------------- 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: 0.7626 moved from start: 0.1845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 4508 Z= 0.321 Angle : 0.611 11.047 6121 Z= 0.311 Chirality : 0.047 0.359 757 Planarity : 0.005 0.043 709 Dihedral : 10.860 74.482 676 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 2.64 % Allowed : 16.06 % Favored : 81.30 % 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: 2.47 (0.36), residues: 548 helix: 2.56 (0.24), residues: 394 sheet: 2.75 (1.44), residues: 14 loop : -1.34 (0.55), residues: 140 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.002 TRP A 54 HIS 0.002 0.000 HIS A 248 PHE 0.014 0.001 PHE A 318 TYR 0.016 0.002 TYR A 280 ARG 0.003 0.000 ARG B 123 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 495 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 86 time to evaluate : 0.463 Fit side-chains REVERT: A 50 LEU cc_start: 0.6840 (tt) cc_final: 0.6277 (tp) REVERT: A 199 MET cc_start: 0.6513 (ttm) cc_final: 0.6146 (ttm) REVERT: B 116 MET cc_start: 0.6803 (tpp) cc_final: 0.6509 (mpp) REVERT: B 174 MET cc_start: 0.7428 (ttm) cc_final: 0.7015 (ttm) REVERT: B 187 ASP cc_start: 0.7466 (t0) cc_final: 0.7193 (t0) REVERT: B 216 CYS cc_start: 0.5825 (t) cc_final: 0.5609 (t) outliers start: 13 outliers final: 9 residues processed: 93 average time/residue: 0.1125 time to fit residues: 14.6411 Evaluate side-chains 94 residues out of total 495 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 85 time to evaluate : 0.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 83 SER Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain B residue 104 LEU Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 181 MET Chi-restraints excluded: chain B residue 249 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 35 optimal weight: 0.3980 chunk 25 optimal weight: 0.0970 chunk 4 optimal weight: 0.9990 chunk 40 optimal weight: 1.9990 chunk 47 optimal weight: 0.0370 chunk 49 optimal weight: 0.0870 chunk 45 optimal weight: 0.0980 chunk 48 optimal weight: 0.8980 chunk 29 optimal weight: 0.5980 chunk 21 optimal weight: 0.0970 chunk 38 optimal weight: 0.9980 overall best weight: 0.0832 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 265 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7567 moved from start: 0.1946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 4508 Z= 0.155 Angle : 0.580 11.248 6121 Z= 0.295 Chirality : 0.043 0.307 757 Planarity : 0.004 0.043 709 Dihedral : 10.456 73.057 676 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 1.63 % Allowed : 17.89 % Favored : 80.49 % 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: 2.58 (0.36), residues: 548 helix: 2.62 (0.24), residues: 395 sheet: 2.71 (1.44), residues: 14 loop : -1.25 (0.57), residues: 139 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.070 0.002 TRP A 54 HIS 0.001 0.000 HIS A 248 PHE 0.013 0.001 PHE A 318 TYR 0.010 0.001 TYR A 280 ARG 0.001 0.000 ARG B 144 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 495 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 88 time to evaluate : 0.484 Fit side-chains revert: symmetry clash REVERT: A 199 MET cc_start: 0.6417 (ttm) cc_final: 0.6048 (ttm) REVERT: A 262 VAL cc_start: 0.8143 (p) cc_final: 0.7931 (p) REVERT: B 116 MET cc_start: 0.6762 (OUTLIER) cc_final: 0.6473 (mpp) REVERT: B 125 SER cc_start: 0.8253 (t) cc_final: 0.7912 (p) REVERT: B 174 MET cc_start: 0.7397 (ttm) cc_final: 0.6961 (ttm) REVERT: B 187 ASP cc_start: 0.7434 (t0) cc_final: 0.7172 (t0) REVERT: B 216 CYS cc_start: 0.5562 (t) cc_final: 0.5347 (t) outliers start: 8 outliers final: 6 residues processed: 92 average time/residue: 0.1140 time to fit residues: 14.6014 Evaluate side-chains 92 residues out of total 495 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 85 time to evaluate : 0.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain B residue 104 LEU Chi-restraints excluded: chain B residue 116 MET Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 249 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 14 optimal weight: 0.7980 chunk 43 optimal weight: 0.4980 chunk 45 optimal weight: 0.3980 chunk 48 optimal weight: 0.9990 chunk 31 optimal weight: 0.0980 chunk 51 optimal weight: 0.0970 chunk 24 optimal weight: 0.0970 chunk 35 optimal weight: 0.2980 chunk 53 optimal weight: 1.9990 chunk 49 optimal weight: 0.5980 chunk 42 optimal weight: 3.9990 overall best weight: 0.1976 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 265 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7569 moved from start: 0.2000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 4508 Z= 0.194 Angle : 0.601 12.283 6121 Z= 0.304 Chirality : 0.044 0.337 757 Planarity : 0.004 0.043 709 Dihedral : 10.326 72.933 676 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 1.83 % Allowed : 17.89 % Favored : 80.28 % 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: 2.45 (0.36), residues: 548 helix: 2.46 (0.24), residues: 397 sheet: 2.91 (1.44), residues: 14 loop : -1.16 (0.58), residues: 137 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.096 0.002 TRP A 54 HIS 0.001 0.000 HIS A 248 PHE 0.013 0.001 PHE A 318 TYR 0.011 0.001 TYR A 280 ARG 0.002 0.000 ARG B 123 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 495 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 85 time to evaluate : 0.488 Fit side-chains REVERT: A 199 MET cc_start: 0.6393 (ttm) cc_final: 0.6022 (ttm) REVERT: A 262 VAL cc_start: 0.8162 (p) cc_final: 0.7956 (p) REVERT: B 116 MET cc_start: 0.6780 (tpp) cc_final: 0.6481 (mpp) REVERT: B 125 SER cc_start: 0.8231 (t) cc_final: 0.7894 (p) REVERT: B 174 MET cc_start: 0.7411 (ttm) cc_final: 0.6966 (ttm) REVERT: B 187 ASP cc_start: 0.7440 (t0) cc_final: 0.7163 (t0) outliers start: 9 outliers final: 8 residues processed: 90 average time/residue: 0.1251 time to fit residues: 15.7464 Evaluate side-chains 92 residues out of total 495 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 84 time to evaluate : 0.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain B residue 104 LEU Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 181 MET Chi-restraints excluded: chain B residue 249 VAL Chi-restraints excluded: chain B residue 322 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 4 optimal weight: 0.7980 chunk 33 optimal weight: 0.9980 chunk 26 optimal weight: 0.9990 chunk 34 optimal weight: 0.0980 chunk 45 optimal weight: 0.9990 chunk 13 optimal weight: 0.8980 chunk 39 optimal weight: 0.5980 chunk 6 optimal weight: 0.6980 chunk 11 optimal weight: 0.9990 chunk 42 optimal weight: 3.9990 chunk 17 optimal weight: 0.0980 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 265 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7607 moved from start: 0.1998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 4508 Z= 0.312 Angle : 0.675 12.288 6121 Z= 0.342 Chirality : 0.047 0.346 757 Planarity : 0.005 0.051 709 Dihedral : 10.533 75.315 676 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 1.83 % Allowed : 17.68 % Favored : 80.49 % 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: 2.33 (0.36), residues: 548 helix: 2.39 (0.24), residues: 394 sheet: 2.89 (1.45), residues: 14 loop : -1.18 (0.56), residues: 140 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.133 0.003 TRP A 54 HIS 0.003 0.001 HIS B 214 PHE 0.012 0.001 PHE A 318 TYR 0.016 0.002 TYR A 280 ARG 0.002 0.000 ARG B 123 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 495 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 87 time to evaluate : 0.462 Fit side-chains REVERT: A 199 MET cc_start: 0.6431 (ttm) cc_final: 0.6057 (ttm) REVERT: B 116 MET cc_start: 0.6860 (tpp) cc_final: 0.6523 (mpp) REVERT: B 174 MET cc_start: 0.7416 (ttm) cc_final: 0.7011 (ttm) REVERT: B 187 ASP cc_start: 0.7453 (t0) cc_final: 0.7156 (t0) REVERT: B 261 MET cc_start: 0.8319 (mmm) cc_final: 0.8102 (mmp) outliers start: 9 outliers final: 8 residues processed: 92 average time/residue: 0.1135 time to fit residues: 14.5025 Evaluate side-chains 94 residues out of total 495 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 86 time to evaluate : 0.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain B residue 104 LEU Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 181 MET Chi-restraints excluded: chain B residue 249 VAL Chi-restraints excluded: chain B residue 322 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 44 optimal weight: 0.0980 chunk 5 optimal weight: 0.0980 chunk 7 optimal weight: 0.5980 chunk 37 optimal weight: 0.3980 chunk 2 optimal weight: 0.5980 chunk 30 optimal weight: 0.4980 chunk 49 optimal weight: 0.8980 chunk 28 optimal weight: 0.2980 chunk 36 optimal weight: 0.0570 chunk 1 optimal weight: 0.8980 chunk 34 optimal weight: 0.0870 overall best weight: 0.1276 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 265 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.149085 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.125861 restraints weight = 6147.340| |-----------------------------------------------------------------------------| r_work (start): 0.3712 rms_B_bonded: 2.15 r_work: 0.3591 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3428 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3428 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7613 moved from start: 0.2100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 4508 Z= 0.184 Angle : 0.675 12.172 6121 Z= 0.340 Chirality : 0.044 0.345 757 Planarity : 0.005 0.055 709 Dihedral : 10.285 74.122 676 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 1.42 % Allowed : 18.09 % Favored : 80.49 % Cbeta Deviations : 0.19 % 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: 2.41 (0.36), residues: 548 helix: 2.45 (0.24), residues: 395 sheet: 2.86 (1.51), residues: 14 loop : -1.19 (0.57), residues: 139 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.144 0.003 TRP A 54 HIS 0.001 0.000 HIS B 214 PHE 0.027 0.001 PHE A 289 TYR 0.011 0.001 TYR A 280 ARG 0.001 0.000 ARG B 144 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1572.37 seconds wall clock time: 28 minutes 58.39 seconds (1738.39 seconds total)