Starting phenix.real_space_refine on Wed Mar 5 23:38:41 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hbv_34644/03_2025/8hbv_34644.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hbv_34644/03_2025/8hbv_34644.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.51 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8hbv_34644/03_2025/8hbv_34644.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hbv_34644/03_2025/8hbv_34644.map" model { file = "/net/cci-nas-00/data/ceres_data/8hbv_34644/03_2025/8hbv_34644.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hbv_34644/03_2025/8hbv_34644.cif" } resolution = 2.51 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= 0.005 sd= 0.118 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 4 5.49 5 S 18 5.16 5 C 2100 2.51 5 N 543 2.21 5 O 614 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 3279 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 2180 Number of conformers: 1 Conformer: "" Number of residues, atoms: 290, 2180 Classifications: {'peptide': 290} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 15, 'TRANS': 274} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 997 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 997 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 3, 'TRANS': 120} Chain: "A" Number of atoms: 102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 102 Unusual residues: {'CDL': 1, 'PC1': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 106 Unresolved non-hydrogen angles: 112 Unresolved non-hydrogen dihedrals: 102 Time building chain proxies: 3.56, per 1000 atoms: 1.09 Number of scatterers: 3279 At special positions: 0 Unit cell: (69.222, 68.388, 110.922, 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 18 16.00 P 4 15.00 O 614 8.00 N 543 7.00 C 2100 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 96 " distance=2.02 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: 1.42 Conformation dependent library (CDL) restraints added in 411.0 milliseconds 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 754 Finding SS restraints... Secondary structure from input PDB file: 13 helices and 3 sheets defined 60.4% alpha, 15.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.32 Creating SS restraints... Processing helix chain 'A' and resid 11 through 42 Proline residue: A 32 - end of helix Processing helix chain 'A' and resid 56 through 69 Processing helix chain 'A' and resid 76 through 105 removed outlier: 4.567A pdb=" N ASP A 96 " --> pdb=" O ILE A 92 " (cutoff:3.500A) removed outlier: 4.950A pdb=" N THR A 97 " --> pdb=" O GLY A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 111 through 143 Proline residue: A 132 - end of helix Processing helix chain 'A' and resid 155 through 168 Processing helix chain 'A' and resid 169 through 174 removed outlier: 3.659A pdb=" N LYS A 174 " --> pdb=" O GLY A 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 175 through 204 Processing helix chain 'A' and resid 210 through 242 removed outlier: 3.563A pdb=" N HIS A 214 " --> pdb=" O ASP A 210 " (cutoff:3.500A) Proline residue: A 231 - end of helix Processing helix chain 'A' and resid 249 through 262 Processing helix chain 'A' and resid 264 through 268 Processing helix chain 'A' and resid 269 through 297 Processing helix chain 'B' and resid 28 through 32 Processing helix chain 'B' and resid 87 through 91 Processing sheet with id=AA1, first strand: chain 'B' and resid 3 through 7 Processing sheet with id=AA2, first strand: chain 'B' and resid 11 through 13 removed outlier: 6.772A pdb=" N VAL B 12 " --> pdb=" O SER B 120 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N MET B 34 " --> pdb=" O ALA B 50 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N ALA B 50 " --> pdb=" O MET B 34 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N TRP B 36 " --> pdb=" O VAL B 48 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 11 through 13 removed outlier: 6.772A pdb=" N VAL B 12 " --> pdb=" O SER B 120 " (cutoff:3.500A) 230 hydrogen bonds defined for protein. 639 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: 0.89 Time building geometry restraints manager: 1.17 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 743 1.33 - 1.45: 730 1.45 - 1.57: 1842 1.57 - 1.69: 8 1.69 - 1.81: 27 Bond restraints: 3350 Sorted by residual: bond pdb=" CA7 CDL A 401 " pdb=" OA8 CDL A 401 " ideal model delta sigma weight residual 1.334 1.455 -0.121 1.10e-02 8.26e+03 1.21e+02 bond pdb=" CB7 CDL A 401 " pdb=" OB8 CDL A 401 " ideal model delta sigma weight residual 1.334 1.443 -0.109 1.10e-02 8.26e+03 9.87e+01 bond pdb=" CA5 CDL A 401 " pdb=" OA6 CDL A 401 " ideal model delta sigma weight residual 1.342 1.453 -0.111 1.50e-02 4.44e+03 5.50e+01 bond pdb=" CB5 CDL A 401 " pdb=" OB6 CDL A 401 " ideal model delta sigma weight residual 1.342 1.446 -0.104 1.50e-02 4.44e+03 4.82e+01 bond pdb=" C21 PC1 A 402 " pdb=" O21 PC1 A 402 " ideal model delta sigma weight residual 1.331 1.455 -0.124 2.00e-02 2.50e+03 3.85e+01 ... (remaining 3345 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.16: 4374 2.16 - 4.33: 113 4.33 - 6.49: 44 6.49 - 8.66: 5 8.66 - 10.82: 5 Bond angle restraints: 4541 Sorted by residual: angle pdb=" C51 CDL A 401 " pdb=" CB5 CDL A 401 " pdb=" OB6 CDL A 401 " ideal model delta sigma weight residual 111.33 120.29 -8.96 1.32e+00 5.72e-01 4.60e+01 angle pdb=" C11 CDL A 401 " pdb=" CA5 CDL A 401 " pdb=" OA6 CDL A 401 " ideal model delta sigma weight residual 111.33 120.24 -8.91 1.32e+00 5.72e-01 4.54e+01 angle pdb=" C71 CDL A 401 " pdb=" CB7 CDL A 401 " pdb=" OB8 CDL A 401 " ideal model delta sigma weight residual 111.64 122.46 -10.82 1.65e+00 3.69e-01 4.32e+01 angle pdb=" C31 CDL A 401 " pdb=" CA7 CDL A 401 " pdb=" OA8 CDL A 401 " ideal model delta sigma weight residual 111.64 121.14 -9.50 1.65e+00 3.69e-01 3.33e+01 angle pdb=" OB8 CDL A 401 " pdb=" CB7 CDL A 401 " pdb=" OB9 CDL A 401 " ideal model delta sigma weight residual 123.94 117.51 6.43 1.21e+00 6.80e-01 2.81e+01 ... (remaining 4536 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.33: 1803 19.33 - 38.67: 147 38.67 - 58.00: 41 58.00 - 77.33: 4 77.33 - 96.66: 4 Dihedral angle restraints: 1999 sinusoidal: 816 harmonic: 1183 Sorted by residual: dihedral pdb=" CA ALA A 208 " pdb=" C ALA A 208 " pdb=" N ASP A 209 " pdb=" CA ASP A 209 " ideal model delta harmonic sigma weight residual -180.00 -161.91 -18.09 0 5.00e+00 4.00e-02 1.31e+01 dihedral pdb=" CA5 CDL A 401 " pdb=" CA4 CDL A 401 " pdb=" OA6 CDL A 401 " pdb=" CA6 CDL A 401 " ideal model delta sinusoidal sigma weight residual 168.24 71.58 96.66 1 3.00e+01 1.11e-03 1.19e+01 dihedral pdb=" CA TRP B 111 " pdb=" C TRP B 111 " pdb=" N GLY B 112 " pdb=" CA GLY B 112 " ideal model delta harmonic sigma weight residual 180.00 163.81 16.19 0 5.00e+00 4.00e-02 1.05e+01 ... (remaining 1996 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 237 0.030 - 0.059: 166 0.059 - 0.089: 64 0.089 - 0.118: 30 0.118 - 0.148: 9 Chirality restraints: 506 Sorted by residual: chirality pdb=" CA THR A 177 " pdb=" N THR A 177 " pdb=" C THR A 177 " pdb=" CB THR A 177 " both_signs ideal model delta sigma weight residual False 2.53 2.38 0.15 2.00e-01 2.50e+01 5.48e-01 chirality pdb=" CA GLU A 167 " pdb=" N GLU A 167 " pdb=" C GLU A 167 " pdb=" CB GLU A 167 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.30e-01 chirality pdb=" CA ARG A 276 " pdb=" N ARG A 276 " pdb=" C ARG A 276 " pdb=" CB ARG A 276 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.76e-01 ... (remaining 503 not shown) Planarity restraints: 566 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE B 101 " 0.022 2.00e-02 2.50e+03 3.04e-02 1.61e+01 pdb=" CG PHE B 101 " -0.069 2.00e-02 2.50e+03 pdb=" CD1 PHE B 101 " 0.030 2.00e-02 2.50e+03 pdb=" CD2 PHE B 101 " 0.017 2.00e-02 2.50e+03 pdb=" CE1 PHE B 101 " -0.007 2.00e-02 2.50e+03 pdb=" CE2 PHE B 101 " 0.006 2.00e-02 2.50e+03 pdb=" CZ PHE B 101 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL A 211 " -0.035 5.00e-02 4.00e+02 5.24e-02 4.39e+00 pdb=" N PRO A 212 " 0.091 5.00e-02 4.00e+02 pdb=" CA PRO A 212 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 212 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS A 9 " -0.024 5.00e-02 4.00e+02 3.66e-02 2.15e+00 pdb=" N PRO A 10 " 0.063 5.00e-02 4.00e+02 pdb=" CA PRO A 10 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 10 " -0.020 5.00e-02 4.00e+02 ... (remaining 563 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 451 2.75 - 3.29: 3118 3.29 - 3.82: 5823 3.82 - 4.36: 6936 4.36 - 4.90: 11855 Nonbonded interactions: 28183 Sorted by model distance: nonbonded pdb=" OE2 GLU A 68 " pdb=" OG SER A 144 " model vdw 2.209 3.040 nonbonded pdb=" O VAL A 14 " pdb=" OG SER A 18 " model vdw 2.272 3.040 nonbonded pdb=" O TRP A 173 " pdb=" OG1 THR A 176 " model vdw 2.283 3.040 nonbonded pdb=" NH1 ARG A 238 " pdb=" OE2 GLU A 261 " model vdw 2.290 3.120 nonbonded pdb=" OD2 ASP B 100 " pdb=" NH1 ARG B 104 " model vdw 2.308 3.120 ... (remaining 28178 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 1.620 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: 0.140 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 14.510 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:14.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8479 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 : 0.009 0.124 3350 Z= 0.609 Angle : 0.961 10.821 4541 Z= 0.500 Chirality : 0.048 0.148 506 Planarity : 0.005 0.052 566 Dihedral : 15.839 96.659 1242 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 0.00 % Allowed : 0.59 % Favored : 99.41 % 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: 1.54 (0.38), residues: 410 helix: 1.88 (0.31), residues: 219 sheet: -0.75 (0.62), residues: 52 loop : 0.50 (0.51), residues: 139 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP A 173 HIS 0.002 0.001 HIS A 9 PHE 0.069 0.004 PHE B 101 TYR 0.016 0.002 TYR A 157 ARG 0.005 0.001 ARG A 293 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 67 time to evaluate : 0.426 Fit side-chains REVERT: A 70 ARG cc_start: 0.7215 (mtt180) cc_final: 0.6688 (ptt90) outliers start: 0 outliers final: 0 residues processed: 67 average time/residue: 1.6311 time to fit residues: 111.6011 Evaluate side-chains 61 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 61 time to evaluate : 0.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 34 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 17 optimal weight: 0.8980 chunk 10 optimal weight: 4.9990 chunk 20 optimal weight: 3.9990 chunk 16 optimal weight: 0.8980 chunk 32 optimal weight: 4.9990 chunk 12 optimal weight: 0.3980 chunk 19 optimal weight: 0.9980 chunk 23 optimal weight: 0.9990 chunk 37 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 59 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.133064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.112617 restraints weight = 3996.582| |-----------------------------------------------------------------------------| r_work (start): 0.3336 rms_B_bonded: 1.28 r_work: 0.3256 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.3166 rms_B_bonded: 3.08 restraints_weight: 0.2500 r_work (final): 0.3166 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8639 moved from start: 0.1238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 3350 Z= 0.250 Angle : 0.536 5.513 4541 Z= 0.278 Chirality : 0.041 0.146 506 Planarity : 0.006 0.057 566 Dihedral : 12.789 71.856 535 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 2.07 % Allowed : 9.47 % Favored : 88.46 % 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: 2.20 (0.39), residues: 410 helix: 2.51 (0.31), residues: 220 sheet: -0.44 (0.65), residues: 52 loop : 0.60 (0.52), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 57 HIS 0.001 0.001 HIS A 147 PHE 0.023 0.002 PHE B 101 TYR 0.013 0.001 TYR A 157 ARG 0.005 0.001 ARG B 72 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 72 time to evaluate : 0.357 Fit side-chains REVERT: A 70 ARG cc_start: 0.7937 (mtt180) cc_final: 0.6749 (ptt90) REVERT: A 91 ARG cc_start: 0.6920 (tmm-80) cc_final: 0.6654 (ptp-170) REVERT: A 115 LYS cc_start: 0.7238 (mtmt) cc_final: 0.7033 (mttt) REVERT: A 117 LEU cc_start: 0.7172 (OUTLIER) cc_final: 0.6776 (mm) REVERT: A 228 MET cc_start: 0.9091 (OUTLIER) cc_final: 0.8856 (mtp) REVERT: A 276 ARG cc_start: 0.8589 (OUTLIER) cc_final: 0.8190 (tmt-80) REVERT: B 106 GLU cc_start: 0.8059 (mp0) cc_final: 0.7846 (pm20) outliers start: 7 outliers final: 2 residues processed: 74 average time/residue: 1.6703 time to fit residues: 126.1877 Evaluate side-chains 70 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 65 time to evaluate : 0.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 228 MET Chi-restraints excluded: chain A residue 276 ARG Chi-restraints excluded: chain B residue 53 SER Chi-restraints excluded: chain B residue 89 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 18 optimal weight: 0.9980 chunk 29 optimal weight: 3.9990 chunk 22 optimal weight: 0.6980 chunk 30 optimal weight: 2.9990 chunk 16 optimal weight: 0.7980 chunk 2 optimal weight: 0.9980 chunk 14 optimal weight: 1.9990 chunk 36 optimal weight: 0.7980 chunk 32 optimal weight: 0.9980 chunk 37 optimal weight: 0.8980 chunk 24 optimal weight: 0.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 77 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.132733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.112590 restraints weight = 3930.862| |-----------------------------------------------------------------------------| r_work (start): 0.3330 rms_B_bonded: 1.27 r_work: 0.3251 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.3163 rms_B_bonded: 3.06 restraints_weight: 0.2500 r_work (final): 0.3163 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8645 moved from start: 0.1476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 3350 Z= 0.246 Angle : 0.518 5.447 4541 Z= 0.268 Chirality : 0.041 0.143 506 Planarity : 0.005 0.052 566 Dihedral : 11.850 58.645 535 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 3.55 % Allowed : 13.61 % Favored : 82.84 % 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: 2.43 (0.40), residues: 410 helix: 2.77 (0.31), residues: 221 sheet: -0.52 (0.65), residues: 54 loop : 0.67 (0.53), residues: 135 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 57 HIS 0.001 0.000 HIS A 147 PHE 0.011 0.002 PHE B 101 TYR 0.015 0.001 TYR A 157 ARG 0.004 0.001 ARG B 72 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 69 time to evaluate : 0.341 Fit side-chains REVERT: A 70 ARG cc_start: 0.7922 (mtt180) cc_final: 0.6758 (ptt90) REVERT: A 115 LYS cc_start: 0.7309 (mtmt) cc_final: 0.7061 (mttt) REVERT: A 117 LEU cc_start: 0.7117 (OUTLIER) cc_final: 0.6701 (mm) REVERT: A 228 MET cc_start: 0.9107 (OUTLIER) cc_final: 0.8901 (mtp) outliers start: 12 outliers final: 5 residues processed: 73 average time/residue: 1.7627 time to fit residues: 131.4357 Evaluate side-chains 71 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 64 time to evaluate : 0.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 LYS Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 167 GLU Chi-restraints excluded: chain A residue 228 MET Chi-restraints excluded: chain A residue 248 LYS Chi-restraints excluded: chain B residue 53 SER Chi-restraints excluded: chain B residue 89 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 32 optimal weight: 0.9990 chunk 6 optimal weight: 3.9990 chunk 25 optimal weight: 0.7980 chunk 22 optimal weight: 0.9990 chunk 7 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 19 optimal weight: 0.0470 chunk 38 optimal weight: 2.9990 chunk 40 optimal weight: 0.7980 chunk 24 optimal weight: 0.3980 chunk 20 optimal weight: 2.9990 overall best weight: 0.6080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.134138 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.113929 restraints weight = 4080.191| |-----------------------------------------------------------------------------| r_work (start): 0.3349 rms_B_bonded: 1.28 r_work: 0.3271 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.3184 rms_B_bonded: 3.10 restraints_weight: 0.2500 r_work (final): 0.3184 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8623 moved from start: 0.1776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 3350 Z= 0.202 Angle : 0.482 5.409 4541 Z= 0.249 Chirality : 0.040 0.137 506 Planarity : 0.005 0.048 566 Dihedral : 11.412 57.701 535 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 2.96 % Allowed : 15.38 % Favored : 81.66 % 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: 2.66 (0.40), residues: 410 helix: 2.96 (0.31), residues: 221 sheet: -0.37 (0.65), residues: 54 loop : 0.75 (0.54), residues: 135 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 57 HIS 0.001 0.000 HIS A 147 PHE 0.008 0.001 PHE A 128 TYR 0.013 0.001 TYR A 157 ARG 0.004 0.000 ARG B 72 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 69 time to evaluate : 0.331 Fit side-chains REVERT: A 70 ARG cc_start: 0.7876 (mtt180) cc_final: 0.6813 (ptt90) REVERT: A 115 LYS cc_start: 0.7225 (mtmt) cc_final: 0.6779 (mtmt) REVERT: A 167 GLU cc_start: 0.8524 (OUTLIER) cc_final: 0.8246 (pm20) REVERT: A 276 ARG cc_start: 0.8547 (OUTLIER) cc_final: 0.8026 (tmt-80) outliers start: 10 outliers final: 5 residues processed: 72 average time/residue: 1.5262 time to fit residues: 112.3494 Evaluate side-chains 71 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 64 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 GLN Chi-restraints excluded: chain A residue 55 LYS Chi-restraints excluded: chain A residue 167 GLU Chi-restraints excluded: chain A residue 248 LYS Chi-restraints excluded: chain A residue 276 ARG Chi-restraints excluded: chain B residue 53 SER Chi-restraints excluded: chain B residue 89 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 33 optimal weight: 0.0070 chunk 30 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 chunk 19 optimal weight: 0.8980 chunk 31 optimal weight: 0.9990 chunk 36 optimal weight: 1.9990 chunk 39 optimal weight: 2.9990 chunk 14 optimal weight: 3.9990 chunk 16 optimal weight: 1.9990 chunk 7 optimal weight: 0.9980 chunk 8 optimal weight: 1.9990 overall best weight: 0.9802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 15 GLN A 214 HIS B 77 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.132476 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.112403 restraints weight = 4029.782| |-----------------------------------------------------------------------------| r_work (start): 0.3329 rms_B_bonded: 1.29 r_work: 0.3251 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.3163 rms_B_bonded: 3.07 restraints_weight: 0.2500 r_work (final): 0.3163 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8651 moved from start: 0.1615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 3350 Z= 0.267 Angle : 0.517 5.419 4541 Z= 0.266 Chirality : 0.041 0.139 506 Planarity : 0.005 0.047 566 Dihedral : 11.670 59.142 535 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 3.25 % Allowed : 17.16 % Favored : 79.59 % 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: 2.56 (0.40), residues: 410 helix: 2.85 (0.31), residues: 221 sheet: -0.36 (0.65), residues: 54 loop : 0.72 (0.53), residues: 135 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 57 HIS 0.001 0.001 HIS B 59 PHE 0.013 0.002 PHE A 17 TYR 0.016 0.001 TYR A 157 ARG 0.004 0.000 ARG B 72 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 67 time to evaluate : 0.386 Fit side-chains REVERT: A 70 ARG cc_start: 0.7892 (mtt180) cc_final: 0.6847 (ptt90) REVERT: A 115 LYS cc_start: 0.7171 (mtmt) cc_final: 0.6701 (mtmt) REVERT: A 167 GLU cc_start: 0.8535 (OUTLIER) cc_final: 0.8258 (pm20) REVERT: A 276 ARG cc_start: 0.8590 (OUTLIER) cc_final: 0.8148 (tmt-80) outliers start: 11 outliers final: 5 residues processed: 71 average time/residue: 1.6247 time to fit residues: 117.8462 Evaluate side-chains 73 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 66 time to evaluate : 0.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 LYS Chi-restraints excluded: chain A residue 167 GLU Chi-restraints excluded: chain A residue 248 LYS Chi-restraints excluded: chain A residue 276 ARG Chi-restraints excluded: chain B residue 25 SER Chi-restraints excluded: chain B residue 53 SER Chi-restraints excluded: chain B residue 89 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 4 optimal weight: 1.9990 chunk 9 optimal weight: 5.9990 chunk 24 optimal weight: 0.6980 chunk 33 optimal weight: 2.9990 chunk 23 optimal weight: 0.5980 chunk 15 optimal weight: 0.9980 chunk 14 optimal weight: 1.9990 chunk 8 optimal weight: 0.8980 chunk 38 optimal weight: 0.7980 chunk 31 optimal weight: 0.9990 chunk 36 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 214 HIS B 77 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.130740 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.110176 restraints weight = 3990.056| |-----------------------------------------------------------------------------| r_work (start): 0.3258 rms_B_bonded: 1.29 r_work: 0.3175 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.3077 rms_B_bonded: 3.07 restraints_weight: 0.2500 r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8601 moved from start: 0.1758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 3350 Z= 0.233 Angle : 0.495 5.393 4541 Z= 0.256 Chirality : 0.040 0.135 506 Planarity : 0.005 0.047 566 Dihedral : 11.397 59.454 535 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 3.55 % Allowed : 17.46 % Favored : 78.99 % 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: 2.63 (0.40), residues: 410 helix: 2.92 (0.31), residues: 221 sheet: -0.37 (0.65), residues: 54 loop : 0.77 (0.53), residues: 135 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 57 HIS 0.001 0.000 HIS A 147 PHE 0.009 0.001 PHE A 128 TYR 0.015 0.001 TYR A 157 ARG 0.004 0.000 ARG B 72 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 68 time to evaluate : 0.456 Fit side-chains REVERT: A 70 ARG cc_start: 0.7887 (mtt180) cc_final: 0.6697 (ptt90) REVERT: A 115 LYS cc_start: 0.7086 (mtmt) cc_final: 0.6638 (mtmt) REVERT: A 167 GLU cc_start: 0.8559 (OUTLIER) cc_final: 0.8293 (pm20) REVERT: A 276 ARG cc_start: 0.8516 (OUTLIER) cc_final: 0.8043 (tmt-80) outliers start: 12 outliers final: 6 residues processed: 72 average time/residue: 5.2285 time to fit residues: 380.8799 Evaluate side-chains 75 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 67 time to evaluate : 1.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 GLN Chi-restraints excluded: chain A residue 55 LYS Chi-restraints excluded: chain A residue 167 GLU Chi-restraints excluded: chain A residue 248 LYS Chi-restraints excluded: chain A residue 276 ARG Chi-restraints excluded: chain B residue 25 SER Chi-restraints excluded: chain B residue 53 SER Chi-restraints excluded: chain B residue 106 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 16 optimal weight: 0.9990 chunk 19 optimal weight: 0.9990 chunk 20 optimal weight: 0.5980 chunk 7 optimal weight: 0.7980 chunk 21 optimal weight: 2.9990 chunk 17 optimal weight: 0.5980 chunk 28 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 3 optimal weight: 0.9980 chunk 8 optimal weight: 3.9990 chunk 12 optimal weight: 1.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 214 HIS B 77 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.130620 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.110135 restraints weight = 3807.424| |-----------------------------------------------------------------------------| r_work (start): 0.3258 rms_B_bonded: 1.27 r_work: 0.3175 rms_B_bonded: 1.78 restraints_weight: 0.5000 r_work: 0.3080 rms_B_bonded: 3.00 restraints_weight: 0.2500 r_work (final): 0.3080 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8599 moved from start: 0.1767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 3350 Z= 0.237 Angle : 0.498 5.388 4541 Z= 0.258 Chirality : 0.040 0.134 506 Planarity : 0.005 0.046 566 Dihedral : 11.273 58.159 535 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 3.55 % Allowed : 18.34 % Favored : 78.11 % 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: 2.63 (0.40), residues: 410 helix: 2.90 (0.31), residues: 221 sheet: -0.34 (0.65), residues: 54 loop : 0.77 (0.53), residues: 135 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 57 HIS 0.001 0.000 HIS B 124 PHE 0.009 0.001 PHE A 128 TYR 0.015 0.001 TYR A 157 ARG 0.005 0.000 ARG A 293 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 67 time to evaluate : 0.382 Fit side-chains REVERT: A 70 ARG cc_start: 0.7863 (mtt180) cc_final: 0.6738 (ptt90) REVERT: A 115 LYS cc_start: 0.7048 (mtmt) cc_final: 0.6598 (mtmt) REVERT: A 167 GLU cc_start: 0.8576 (OUTLIER) cc_final: 0.8282 (pm20) REVERT: A 276 ARG cc_start: 0.8513 (OUTLIER) cc_final: 0.8040 (tmt-80) outliers start: 12 outliers final: 6 residues processed: 71 average time/residue: 1.5505 time to fit residues: 112.5534 Evaluate side-chains 74 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 66 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 GLN Chi-restraints excluded: chain A residue 167 GLU Chi-restraints excluded: chain A residue 248 LYS Chi-restraints excluded: chain A residue 276 ARG Chi-restraints excluded: chain B residue 25 SER Chi-restraints excluded: chain B residue 53 SER Chi-restraints excluded: chain B residue 89 GLU Chi-restraints excluded: chain B residue 106 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 37 optimal weight: 1.9990 chunk 2 optimal weight: 0.9990 chunk 18 optimal weight: 0.8980 chunk 34 optimal weight: 1.9990 chunk 11 optimal weight: 0.9980 chunk 1 optimal weight: 0.7980 chunk 38 optimal weight: 1.9990 chunk 4 optimal weight: 0.7980 chunk 35 optimal weight: 0.6980 chunk 20 optimal weight: 4.9990 chunk 7 optimal weight: 0.0570 overall best weight: 0.6498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 77 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.131533 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.111105 restraints weight = 3892.362| |-----------------------------------------------------------------------------| r_work (start): 0.3272 rms_B_bonded: 1.28 r_work: 0.3188 rms_B_bonded: 1.81 restraints_weight: 0.5000 r_work: 0.3093 rms_B_bonded: 3.03 restraints_weight: 0.2500 r_work (final): 0.3093 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8587 moved from start: 0.1932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 3350 Z= 0.208 Angle : 0.480 5.381 4541 Z= 0.249 Chirality : 0.039 0.132 506 Planarity : 0.005 0.045 566 Dihedral : 10.996 59.784 535 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 2.96 % Allowed : 19.53 % Favored : 77.51 % 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: 2.74 (0.40), residues: 410 helix: 2.99 (0.31), residues: 221 sheet: -0.21 (0.66), residues: 54 loop : 0.78 (0.53), residues: 135 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 57 HIS 0.001 0.000 HIS B 124 PHE 0.008 0.001 PHE A 128 TYR 0.014 0.001 TYR A 157 ARG 0.005 0.000 ARG A 293 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 70 time to evaluate : 0.384 Fit side-chains REVERT: A 70 ARG cc_start: 0.7890 (mtt180) cc_final: 0.6739 (ptt90) REVERT: A 115 LYS cc_start: 0.7075 (mtmt) cc_final: 0.6626 (mtmt) REVERT: A 167 GLU cc_start: 0.8525 (OUTLIER) cc_final: 0.8293 (pm20) REVERT: A 276 ARG cc_start: 0.8517 (OUTLIER) cc_final: 0.7976 (tmt-80) REVERT: B 43 LYS cc_start: 0.8041 (mtmt) cc_final: 0.7789 (mtmt) outliers start: 10 outliers final: 6 residues processed: 73 average time/residue: 1.9877 time to fit residues: 147.9037 Evaluate side-chains 75 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 67 time to evaluate : 0.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 GLN Chi-restraints excluded: chain A residue 116 ILE Chi-restraints excluded: chain A residue 167 GLU Chi-restraints excluded: chain A residue 248 LYS Chi-restraints excluded: chain A residue 276 ARG Chi-restraints excluded: chain B residue 25 SER Chi-restraints excluded: chain B residue 53 SER Chi-restraints excluded: chain B residue 106 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 33 optimal weight: 0.0570 chunk 29 optimal weight: 3.9990 chunk 17 optimal weight: 0.5980 chunk 36 optimal weight: 0.8980 chunk 40 optimal weight: 0.7980 chunk 11 optimal weight: 0.9990 chunk 31 optimal weight: 0.9980 chunk 26 optimal weight: 2.9990 chunk 14 optimal weight: 0.9990 chunk 38 optimal weight: 0.6980 chunk 21 optimal weight: 2.9990 overall best weight: 0.6098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 77 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.131769 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.111411 restraints weight = 3941.984| |-----------------------------------------------------------------------------| r_work (start): 0.3276 rms_B_bonded: 1.28 r_work: 0.3193 rms_B_bonded: 1.80 restraints_weight: 0.5000 r_work: 0.3096 rms_B_bonded: 3.05 restraints_weight: 0.2500 r_work (final): 0.3096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8584 moved from start: 0.1968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 3350 Z= 0.202 Angle : 0.477 5.371 4541 Z= 0.247 Chirality : 0.039 0.132 506 Planarity : 0.005 0.045 566 Dihedral : 10.808 59.359 535 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 2.96 % Allowed : 19.23 % Favored : 77.81 % 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: 2.82 (0.40), residues: 410 helix: 3.01 (0.31), residues: 221 sheet: -0.03 (0.66), residues: 54 loop : 0.81 (0.53), residues: 135 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 57 HIS 0.001 0.000 HIS B 124 PHE 0.008 0.001 PHE A 128 TYR 0.014 0.001 TYR A 157 ARG 0.006 0.000 ARG A 293 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 68 time to evaluate : 0.343 Fit side-chains REVERT: A 70 ARG cc_start: 0.7890 (mtt180) cc_final: 0.6740 (ptt90) REVERT: A 115 LYS cc_start: 0.7074 (mtmt) cc_final: 0.6628 (mtmt) REVERT: A 167 GLU cc_start: 0.8518 (OUTLIER) cc_final: 0.8302 (pm20) REVERT: A 276 ARG cc_start: 0.8513 (OUTLIER) cc_final: 0.7975 (tmt-80) outliers start: 10 outliers final: 7 residues processed: 71 average time/residue: 1.5350 time to fit residues: 111.3512 Evaluate side-chains 75 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 66 time to evaluate : 0.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 GLN Chi-restraints excluded: chain A residue 116 ILE Chi-restraints excluded: chain A residue 167 GLU Chi-restraints excluded: chain A residue 248 LYS Chi-restraints excluded: chain A residue 276 ARG Chi-restraints excluded: chain B residue 25 SER Chi-restraints excluded: chain B residue 53 SER Chi-restraints excluded: chain B residue 89 GLU Chi-restraints excluded: chain B residue 106 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 2 optimal weight: 0.9990 chunk 22 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 32 optimal weight: 0.9990 chunk 29 optimal weight: 2.9990 chunk 25 optimal weight: 0.6980 chunk 16 optimal weight: 0.6980 chunk 0 optimal weight: 3.9990 chunk 4 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 14 optimal weight: 3.9990 overall best weight: 1.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 214 HIS B 77 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.129787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.109319 restraints weight = 3843.496| |-----------------------------------------------------------------------------| r_work (start): 0.3248 rms_B_bonded: 1.27 r_work: 0.3165 rms_B_bonded: 1.79 restraints_weight: 0.5000 r_work: 0.3067 rms_B_bonded: 3.01 restraints_weight: 0.2500 r_work (final): 0.3067 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8616 moved from start: 0.1788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 3350 Z= 0.286 Angle : 0.530 5.401 4541 Z= 0.273 Chirality : 0.041 0.134 506 Planarity : 0.005 0.046 566 Dihedral : 11.145 59.988 535 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 2.96 % Allowed : 18.93 % Favored : 78.11 % 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: 2.63 (0.39), residues: 410 helix: 2.83 (0.31), residues: 221 sheet: -0.08 (0.67), residues: 54 loop : 0.77 (0.53), residues: 135 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 57 HIS 0.002 0.001 HIS B 59 PHE 0.012 0.002 PHE A 128 TYR 0.018 0.001 TYR A 157 ARG 0.006 0.001 ARG A 293 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 64 time to evaluate : 0.402 Fit side-chains REVERT: A 70 ARG cc_start: 0.7919 (mtt180) cc_final: 0.6713 (ptt90) REVERT: A 115 LYS cc_start: 0.7100 (mtmt) cc_final: 0.6628 (mtmt) REVERT: A 167 GLU cc_start: 0.8633 (OUTLIER) cc_final: 0.8301 (pm20) REVERT: A 276 ARG cc_start: 0.8567 (OUTLIER) cc_final: 0.8109 (tmt-80) outliers start: 10 outliers final: 6 residues processed: 67 average time/residue: 1.6275 time to fit residues: 111.4071 Evaluate side-chains 71 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 63 time to evaluate : 0.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 GLN Chi-restraints excluded: chain A residue 167 GLU Chi-restraints excluded: chain A residue 248 LYS Chi-restraints excluded: chain A residue 276 ARG Chi-restraints excluded: chain B residue 25 SER Chi-restraints excluded: chain B residue 53 SER Chi-restraints excluded: chain B residue 89 GLU Chi-restraints excluded: chain B residue 106 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 35 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 34 optimal weight: 0.7980 chunk 19 optimal weight: 0.0470 chunk 36 optimal weight: 0.7980 chunk 32 optimal weight: 2.9990 chunk 13 optimal weight: 0.4980 chunk 26 optimal weight: 1.9990 chunk 22 optimal weight: 0.7980 chunk 10 optimal weight: 0.0970 chunk 16 optimal weight: 0.8980 overall best weight: 0.4476 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 77 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.132761 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.112501 restraints weight = 3878.164| |-----------------------------------------------------------------------------| r_work (start): 0.3291 rms_B_bonded: 1.28 r_work: 0.3209 rms_B_bonded: 1.80 restraints_weight: 0.5000 r_work: 0.3114 rms_B_bonded: 3.04 restraints_weight: 0.2500 r_work (final): 0.3114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8564 moved from start: 0.2136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 3350 Z= 0.177 Angle : 0.463 5.341 4541 Z= 0.240 Chirality : 0.039 0.129 506 Planarity : 0.005 0.046 566 Dihedral : 10.587 59.558 535 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 2.66 % Allowed : 19.53 % Favored : 77.81 % 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: 2.87 (0.40), residues: 410 helix: 3.06 (0.31), residues: 221 sheet: 0.29 (0.74), residues: 46 loop : 0.66 (0.51), residues: 143 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 57 HIS 0.001 0.000 HIS B 59 PHE 0.007 0.001 PHE B 27 TYR 0.011 0.001 TYR A 157 ARG 0.006 0.000 ARG A 293 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4167.73 seconds wall clock time: 73 minutes 25.07 seconds (4405.07 seconds total)