Starting phenix.real_space_refine on Fri May 9 22:41:11 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hbv_34644/05_2025/8hbv_34644.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hbv_34644/05_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_34644/05_2025/8hbv_34644.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hbv_34644/05_2025/8hbv_34644.map" model { file = "/net/cci-nas-00/data/ceres_data/8hbv_34644/05_2025/8hbv_34644.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hbv_34644/05_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-5687/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: 3.17, per 1000 atoms: 0.97 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: 0.89 Conformation dependent library (CDL) restraints added in 369.3 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: 0.31 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: 1.00 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: 1.150 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 12.790 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:11.540 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: 0.8479 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 3351 Z= 0.506 Angle : 0.964 10.821 4543 Z= 0.501 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 Details of bonding type rmsd hydrogen bonds : bond 0.09123 ( 226) hydrogen bonds : angle 7.27625 ( 639) SS BOND : bond 0.00613 ( 1) SS BOND : angle 3.42459 ( 2) covalent geometry : bond 0.00941 ( 3350) covalent geometry : angle 0.96139 ( 4541) *********************** 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 : 0.366 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: 1.6535 time to fit residues: 113.1122 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 : 0.337 ------------------------------------------------------------------------------- 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: 0.3167 rms_B_bonded: 3.07 restraints_weight: 0.2500 r_work (final): 0.3167 ------------------------------------------------------------------------------- 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 3351 Z= 0.157 Angle : 0.537 5.513 4543 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 Details of bonding type rmsd hydrogen bonds : bond 0.03794 ( 226) hydrogen bonds : angle 5.70701 ( 639) SS BOND : bond 0.00366 ( 1) SS BOND : angle 1.94726 ( 2) covalent geometry : bond 0.00370 ( 3350) covalent geometry : angle 0.53555 ( 4541) *********************** 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 : 0.354 Fit side-chains REVERT: A 70 ARG cc_start: 0.7945 (mtt180) cc_final: 0.6754 (ptt90) REVERT: A 91 ARG cc_start: 0.6941 (tmm-80) cc_final: 0.6671 (ptp-170) REVERT: A 115 LYS cc_start: 0.7268 (mtmt) cc_final: 0.7067 (mttt) REVERT: A 117 LEU cc_start: 0.7195 (OUTLIER) cc_final: 0.6800 (mm) REVERT: A 228 MET cc_start: 0.9097 (OUTLIER) cc_final: 0.8863 (mtp) REVERT: A 276 ARG cc_start: 0.8591 (OUTLIER) cc_final: 0.8194 (tmt-80) REVERT: B 106 GLU cc_start: 0.8059 (mp0) cc_final: 0.7847 (pm20) outliers start: 7 outliers final: 2 residues processed: 74 average time/residue: 1.6296 time to fit residues: 123.2282 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 : 0.335 ------------------------------------------------------------------------------- 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: 0.7980 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: 0.8980 chunk 37 optimal weight: 0.8980 chunk 24 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 77 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.132651 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.112447 restraints weight = 3951.583| |-----------------------------------------------------------------------------| r_work (start): 0.3335 rms_B_bonded: 1.27 r_work: 0.3256 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.3167 rms_B_bonded: 3.09 restraints_weight: 0.2500 r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8640 moved from start: 0.1507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 3351 Z= 0.147 Angle : 0.510 5.440 4543 Z= 0.264 Chirality : 0.041 0.142 506 Planarity : 0.005 0.051 566 Dihedral : 11.814 57.703 535 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 3.85 % Allowed : 13.91 % Favored : 82.25 % 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 (0.40), residues: 410 helix: 2.80 (0.31), residues: 221 sheet: -0.51 (0.65), residues: 54 loop : 0.69 (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 B 59 PHE 0.012 0.002 PHE B 101 TYR 0.014 0.001 TYR A 157 ARG 0.004 0.001 ARG B 72 Details of bonding type rmsd hydrogen bonds : bond 0.03607 ( 226) hydrogen bonds : angle 5.47251 ( 639) SS BOND : bond 0.00353 ( 1) SS BOND : angle 1.48877 ( 2) covalent geometry : bond 0.00346 ( 3350) covalent geometry : angle 0.50904 ( 4541) *********************** 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 83 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 70 time to evaluate : 0.384 Fit side-chains REVERT: A 70 ARG cc_start: 0.7912 (mtt180) cc_final: 0.6758 (ptt90) REVERT: A 115 LYS cc_start: 0.7279 (mtmt) cc_final: 0.7034 (mttt) REVERT: A 117 LEU cc_start: 0.7091 (OUTLIER) cc_final: 0.6680 (mm) REVERT: A 276 ARG cc_start: 0.8565 (OUTLIER) cc_final: 0.8134 (tmt-80) outliers start: 13 outliers final: 5 residues processed: 74 average time/residue: 1.5404 time to fit residues: 116.5220 Evaluate side-chains 72 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 65 time to evaluate : 0.327 ------------------------------------------------------------------------------- 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 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=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: 0.6980 chunk 22 optimal weight: 1.9990 chunk 7 optimal weight: 0.7980 chunk 28 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 40 optimal weight: 0.7980 chunk 24 optimal weight: 0.6980 chunk 20 optimal weight: 0.3980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.3594 r_free = 0.3594 target = 0.133775 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.113597 restraints weight = 4079.032| |-----------------------------------------------------------------------------| r_work (start): 0.3344 rms_B_bonded: 1.28 r_work: 0.3266 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.3177 rms_B_bonded: 3.10 restraints_weight: 0.2500 r_work (final): 0.3177 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8630 moved from start: 0.1686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 3351 Z= 0.136 Angle : 0.491 5.416 4543 Z= 0.254 Chirality : 0.040 0.138 506 Planarity : 0.005 0.048 566 Dihedral : 11.458 57.435 535 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 2.37 % Allowed : 15.68 % Favored : 81.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.63 (0.40), residues: 410 helix: 2.93 (0.31), residues: 221 sheet: -0.41 (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 0.016 0.001 PHE A 17 TYR 0.014 0.001 TYR A 157 ARG 0.004 0.000 ARG B 72 Details of bonding type rmsd hydrogen bonds : bond 0.03437 ( 226) hydrogen bonds : angle 5.31241 ( 639) SS BOND : bond 0.00239 ( 1) SS BOND : angle 1.26579 ( 2) covalent geometry : bond 0.00319 ( 3350) covalent geometry : angle 0.49065 ( 4541) *********************** 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 76 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 68 time to evaluate : 0.372 Fit side-chains REVERT: A 70 ARG cc_start: 0.7873 (mtt180) cc_final: 0.6824 (ptt90) REVERT: A 115 LYS cc_start: 0.7192 (mtmt) cc_final: 0.6740 (mtmt) REVERT: A 167 GLU cc_start: 0.8531 (OUTLIER) cc_final: 0.8230 (pm20) outliers start: 8 outliers final: 5 residues processed: 71 average time/residue: 1.5067 time to fit residues: 109.3508 Evaluate side-chains 69 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 63 time to evaluate : 0.322 ------------------------------------------------------------------------------- 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 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: 0.0010 chunk 30 optimal weight: 0.9990 chunk 12 optimal weight: 0.8980 chunk 19 optimal weight: 0.6980 chunk 31 optimal weight: 0.9980 chunk 36 optimal weight: 0.7980 chunk 39 optimal weight: 0.0870 chunk 14 optimal weight: 2.9990 chunk 16 optimal weight: 0.5980 chunk 7 optimal weight: 0.9990 chunk 8 optimal weight: 2.9990 overall best weight: 0.4364 ------------------------------------------------------------------------------- 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 = 0.3556 r_free = 0.3556 target = 0.133241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.112984 restraints weight = 3946.599| |-----------------------------------------------------------------------------| r_work (start): 0.3296 rms_B_bonded: 1.26 r_work: 0.3216 rms_B_bonded: 1.77 restraints_weight: 0.5000 r_work: 0.3122 rms_B_bonded: 2.97 restraints_weight: 0.2500 r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8550 moved from start: 0.1987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 3351 Z= 0.111 Angle : 0.461 5.345 4543 Z= 0.238 Chirality : 0.039 0.134 506 Planarity : 0.005 0.045 566 Dihedral : 11.037 59.293 535 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 2.66 % Allowed : 17.75 % 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: 2.84 (0.40), residues: 410 helix: 3.11 (0.31), residues: 221 sheet: -0.23 (0.65), residues: 54 loop : 0.79 (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 0.007 0.001 PHE B 27 TYR 0.011 0.001 TYR A 157 ARG 0.004 0.000 ARG A 293 Details of bonding type rmsd hydrogen bonds : bond 0.03171 ( 226) hydrogen bonds : angle 5.08165 ( 639) SS BOND : bond 0.00257 ( 1) SS BOND : angle 1.00314 ( 2) covalent geometry : bond 0.00256 ( 3350) covalent geometry : angle 0.46012 ( 4541) *********************** 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 77 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 68 time to evaluate : 0.309 Fit side-chains REVERT: A 70 ARG cc_start: 0.7836 (mtt180) cc_final: 0.6656 (ptt90) REVERT: A 115 LYS cc_start: 0.7048 (mtmt) cc_final: 0.6592 (mtmt) REVERT: A 167 GLU cc_start: 0.8485 (OUTLIER) cc_final: 0.8255 (pm20) REVERT: A 276 ARG cc_start: 0.8491 (OUTLIER) cc_final: 0.7941 (tmt-80) outliers start: 9 outliers final: 2 residues processed: 71 average time/residue: 1.5086 time to fit residues: 109.5202 Evaluate side-chains 70 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 66 time to evaluate : 0.358 ------------------------------------------------------------------------------- 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 276 ARG Chi-restraints excluded: chain B residue 53 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 4 optimal weight: 4.9990 chunk 9 optimal weight: 6.9990 chunk 24 optimal weight: 0.8980 chunk 33 optimal weight: 0.0670 chunk 23 optimal weight: 0.0970 chunk 15 optimal weight: 2.9990 chunk 14 optimal weight: 2.9990 chunk 8 optimal weight: 0.8980 chunk 38 optimal weight: 1.9990 chunk 31 optimal weight: 0.9990 chunk 36 optimal weight: 0.3980 overall best weight: 0.4716 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 15 GLN B 77 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.133234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.112735 restraints weight = 3999.913| |-----------------------------------------------------------------------------| r_work (start): 0.3294 rms_B_bonded: 1.30 r_work: 0.3211 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.3114 rms_B_bonded: 3.08 restraints_weight: 0.2500 r_work (final): 0.3114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8566 moved from start: 0.2031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 3351 Z= 0.114 Angle : 0.462 5.328 4543 Z= 0.238 Chirality : 0.039 0.132 506 Planarity : 0.005 0.044 566 Dihedral : 10.835 58.081 535 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 2.07 % Allowed : 19.82 % 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: 2.95 (0.40), residues: 410 helix: 3.15 (0.31), residues: 221 sheet: 0.06 (0.67), residues: 54 loop : 0.81 (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 0.012 0.001 PHE A 17 TYR 0.010 0.001 TYR A 157 ARG 0.005 0.000 ARG A 293 Details of bonding type rmsd hydrogen bonds : bond 0.03162 ( 226) hydrogen bonds : angle 5.01625 ( 639) SS BOND : bond 0.00251 ( 1) SS BOND : angle 1.07151 ( 2) covalent geometry : bond 0.00266 ( 3350) covalent geometry : angle 0.46137 ( 4541) *********************** 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 77 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 70 time to evaluate : 0.352 Fit side-chains REVERT: A 70 ARG cc_start: 0.7872 (mtt180) cc_final: 0.6705 (ptt90) REVERT: A 115 LYS cc_start: 0.7062 (mtmt) cc_final: 0.6608 (mtmt) REVERT: B 106 GLU cc_start: 0.7990 (OUTLIER) cc_final: 0.7582 (pm20) outliers start: 7 outliers final: 2 residues processed: 72 average time/residue: 1.5604 time to fit residues: 114.8736 Evaluate side-chains 66 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 63 time to evaluate : 0.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 LYS 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: 0.6980 chunk 19 optimal weight: 1.9990 chunk 20 optimal weight: 0.7980 chunk 7 optimal weight: 0.6980 chunk 21 optimal weight: 1.9990 chunk 17 optimal weight: 0.6980 chunk 28 optimal weight: 1.9990 chunk 0 optimal weight: 0.5980 chunk 3 optimal weight: 0.1980 chunk 8 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 15 GLN B 77 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.132479 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.112058 restraints weight = 3807.924| |-----------------------------------------------------------------------------| r_work (start): 0.3285 rms_B_bonded: 1.27 r_work: 0.3203 rms_B_bonded: 1.79 restraints_weight: 0.5000 r_work: 0.3108 rms_B_bonded: 3.00 restraints_weight: 0.2500 r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8570 moved from start: 0.2053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 3351 Z= 0.124 Angle : 0.477 5.341 4543 Z= 0.247 Chirality : 0.039 0.130 506 Planarity : 0.005 0.044 566 Dihedral : 10.817 59.387 535 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 2.07 % Allowed : 19.82 % 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: 2.92 (0.40), residues: 410 helix: 3.08 (0.31), residues: 221 sheet: 0.20 (0.68), residues: 54 loop : 0.80 (0.52), residues: 135 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 A 128 TYR 0.011 0.001 TYR A 157 ARG 0.005 0.000 ARG A 293 Details of bonding type rmsd hydrogen bonds : bond 0.03269 ( 226) hydrogen bonds : angle 5.08211 ( 639) SS BOND : bond 0.00224 ( 1) SS BOND : angle 1.14318 ( 2) covalent geometry : bond 0.00293 ( 3350) covalent geometry : angle 0.47681 ( 4541) *********************** 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 72 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 65 time to evaluate : 0.327 Fit side-chains REVERT: A 70 ARG cc_start: 0.7872 (mtt180) cc_final: 0.6736 (ptt90) REVERT: A 115 LYS cc_start: 0.7078 (mtmt) cc_final: 0.6622 (mtmt) REVERT: B 106 GLU cc_start: 0.7968 (OUTLIER) cc_final: 0.7553 (pm20) outliers start: 7 outliers final: 3 residues processed: 69 average time/residue: 1.5170 time to fit residues: 106.9734 Evaluate side-chains 70 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 66 time to evaluate : 0.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 LYS 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 37 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 18 optimal weight: 0.8980 chunk 34 optimal weight: 3.9990 chunk 11 optimal weight: 0.9990 chunk 1 optimal weight: 0.7980 chunk 38 optimal weight: 2.9990 chunk 4 optimal weight: 0.7980 chunk 35 optimal weight: 0.9980 chunk 20 optimal weight: 0.2980 chunk 7 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.3538 r_free = 0.3538 target = 0.131632 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.111120 restraints weight = 3887.252| |-----------------------------------------------------------------------------| r_work (start): 0.3273 rms_B_bonded: 1.29 r_work: 0.3190 rms_B_bonded: 1.80 restraints_weight: 0.5000 r_work: 0.3094 rms_B_bonded: 3.03 restraints_weight: 0.2500 r_work (final): 0.3094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8584 moved from start: 0.1988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 3351 Z= 0.137 Angle : 0.489 5.361 4543 Z= 0.252 Chirality : 0.040 0.130 506 Planarity : 0.005 0.044 566 Dihedral : 10.834 59.593 535 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 1.48 % Allowed : 20.12 % Favored : 78.40 % 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 (0.39), residues: 410 helix: 3.03 (0.31), residues: 221 sheet: 0.18 (0.68), residues: 54 loop : 0.80 (0.52), 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 0.013 0.001 TYR A 157 ARG 0.005 0.000 ARG A 293 Details of bonding type rmsd hydrogen bonds : bond 0.03383 ( 226) hydrogen bonds : angle 5.15577 ( 639) SS BOND : bond 0.00248 ( 1) SS BOND : angle 1.22453 ( 2) covalent geometry : bond 0.00322 ( 3350) covalent geometry : angle 0.48813 ( 4541) *********************** 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 72 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 67 time to evaluate : 0.369 Fit side-chains REVERT: A 70 ARG cc_start: 0.7907 (mtt180) cc_final: 0.6751 (ptt90) REVERT: A 115 LYS cc_start: 0.7062 (mtmt) cc_final: 0.6612 (mtmt) REVERT: B 106 GLU cc_start: 0.8003 (OUTLIER) cc_final: 0.7562 (pm20) outliers start: 5 outliers final: 3 residues processed: 70 average time/residue: 1.5362 time to fit residues: 109.9717 Evaluate side-chains 70 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 66 time to evaluate : 0.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 LYS 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 ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 56.5121 > 50: distance: 44 - 61: 3.867 distance: 48 - 66: 6.370 distance: 52 - 70: 14.870 distance: 57 - 78: 28.965 distance: 64 - 85: 7.327 distance: 66 - 67: 4.972 distance: 67 - 68: 7.124 distance: 68 - 69: 4.159 distance: 68 - 70: 6.626 distance: 69 - 92: 7.015 distance: 70 - 71: 5.640 distance: 71 - 72: 6.329 distance: 71 - 74: 9.689 distance: 72 - 73: 5.291 distance: 72 - 78: 13.648 distance: 73 - 96: 9.499 distance: 74 - 75: 11.177 distance: 75 - 76: 16.719 distance: 75 - 77: 6.775 distance: 78 - 79: 29.272 distance: 79 - 80: 6.127 distance: 79 - 82: 15.353 distance: 80 - 81: 7.127 distance: 80 - 85: 8.800 distance: 81 - 100: 3.852 distance: 82 - 83: 15.879 distance: 82 - 84: 15.492 distance: 85 - 86: 3.949 distance: 86 - 89: 5.178 distance: 88 - 107: 8.638 distance: 89 - 91: 4.607 distance: 92 - 93: 3.639 distance: 94 - 95: 4.330 distance: 94 - 96: 3.078 distance: 95 - 112: 5.346 distance: 96 - 97: 3.871 distance: 98 - 99: 3.859 distance: 98 - 100: 5.523 distance: 99 - 119: 6.600 distance: 100 - 101: 4.655 distance: 101 - 102: 3.889 distance: 101 - 104: 4.442 distance: 103 - 125: 4.642 distance: 104 - 105: 3.769 distance: 104 - 106: 7.113 distance: 108 - 109: 4.032 distance: 109 - 110: 4.601 distance: 110 - 133: 6.549 distance: 112 - 113: 3.906 distance: 115 - 137: 4.791 distance: 116 - 118: 4.112