Starting phenix.real_space_refine on Mon Jan 13 19:57:15 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7xos_33358/01_2025/7xos_33358.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xos_33358/01_2025/7xos_33358.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7xos_33358/01_2025/7xos_33358.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xos_33358/01_2025/7xos_33358.map" model { file = "/net/cci-nas-00/data/ceres_data/7xos_33358/01_2025/7xos_33358.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xos_33358/01_2025/7xos_33358.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.006 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: 4 Type Number sf(0) Gaussians S 20 5.16 5 C 2397 2.51 5 N 665 2.21 5 O 773 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 3855 Number of models: 1 Model: "" Number of chains: 1 Chain: "K" Number of atoms: 3855 Number of conformers: 1 Conformer: "" Number of residues, atoms: 524, 3855 Classifications: {'peptide': 524} Link IDs: {'PTRANS': 14, 'TRANS': 509} Time building chain proxies: 2.82, per 1000 atoms: 0.73 Number of scatterers: 3855 At special positions: 0 Unit cell: (73.08, 88.74, 69.6, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 20 16.00 O 773 8.00 N 665 7.00 C 2397 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 1.02 Conformation dependent library (CDL) restraints added in 464.4 milliseconds 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 948 Finding SS restraints... Secondary structure from input PDB file: 20 helices and 7 sheets defined 59.2% alpha, 11.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.43 Creating SS restraints... Processing helix chain 'K' and resid 9 through 28 Processing helix chain 'K' and resid 29 through 31 No H-bonds generated for 'chain 'K' and resid 29 through 31' Processing helix chain 'K' and resid 52 through 59 removed outlier: 3.805A pdb=" N VAL K 56 " --> pdb=" O ASP K 52 " (cutoff:3.500A) Processing helix chain 'K' and resid 64 through 86 Processing helix chain 'K' and resid 88 through 109 Processing helix chain 'K' and resid 112 through 135 Processing helix chain 'K' and resid 140 through 152 Processing helix chain 'K' and resid 155 through 170 Processing helix chain 'K' and resid 201 through 205 removed outlier: 3.700A pdb=" N ILE K 205 " --> pdb=" O PRO K 202 " (cutoff:3.500A) Processing helix chain 'K' and resid 233 through 244 removed outlier: 3.630A pdb=" N LEU K 237 " --> pdb=" O MET K 233 " (cutoff:3.500A) Processing helix chain 'K' and resid 256 through 268 removed outlier: 4.086A pdb=" N ALA K 260 " --> pdb=" O GLY K 256 " (cutoff:3.500A) Processing helix chain 'K' and resid 283 through 297 Processing helix chain 'K' and resid 338 through 355 removed outlier: 3.863A pdb=" N ILE K 342 " --> pdb=" O GLU K 338 " (cutoff:3.500A) Processing helix chain 'K' and resid 358 through 375 removed outlier: 4.299A pdb=" N GLY K 375 " --> pdb=" O LYS K 371 " (cutoff:3.500A) Processing helix chain 'K' and resid 385 through 409 Processing helix chain 'K' and resid 416 through 426 Processing helix chain 'K' and resid 433 through 459 Proline residue: K 450 - end of helix Processing helix chain 'K' and resid 461 through 472 removed outlier: 4.131A pdb=" N VAL K 465 " --> pdb=" O GLU K 461 " (cutoff:3.500A) Processing helix chain 'K' and resid 488 through 492 Processing helix chain 'K' and resid 497 through 516 Processing sheet with id=AA1, first strand: chain 'K' and resid 4 through 8 Processing sheet with id=AA2, first strand: chain 'K' and resid 38 through 40 Processing sheet with id=AA3, first strand: chain 'K' and resid 174 through 179 Processing sheet with id=AA4, first strand: chain 'K' and resid 193 through 195 Processing sheet with id=AA5, first strand: chain 'K' and resid 219 through 222 removed outlier: 6.268A pdb=" N PHE K 219 " --> pdb=" O LEU K 248 " (cutoff:3.500A) removed outlier: 7.799A pdb=" N ILE K 250 " --> pdb=" O PHE K 219 " (cutoff:3.500A) removed outlier: 5.927A pdb=" N LEU K 221 " --> pdb=" O ILE K 250 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ALA K 251 " --> pdb=" O VAL K 276 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'K' and resid 411 through 413 Processing sheet with id=AA7, first strand: chain 'K' and resid 476 through 479 262 hydrogen bonds defined for protein. 756 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.14 Time building geometry restraints manager: 1.14 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1312 1.34 - 1.45: 243 1.45 - 1.57: 2291 1.57 - 1.69: 0 1.69 - 1.81: 37 Bond restraints: 3883 Sorted by residual: bond pdb=" CG1 ILE K 353 " pdb=" CD1 ILE K 353 " ideal model delta sigma weight residual 1.513 1.471 0.042 3.90e-02 6.57e+02 1.14e+00 bond pdb=" CA ALA K 449 " pdb=" C ALA K 449 " ideal model delta sigma weight residual 1.520 1.530 -0.010 1.23e-02 6.61e+03 6.60e-01 bond pdb=" N GLU K 354 " pdb=" CA GLU K 354 " ideal model delta sigma weight residual 1.457 1.467 -0.010 1.40e-02 5.10e+03 5.32e-01 bond pdb=" C VAL K 169 " pdb=" O VAL K 169 " ideal model delta sigma weight residual 1.230 1.242 -0.013 1.78e-02 3.16e+03 5.14e-01 bond pdb=" C VAL K 27 " pdb=" O VAL K 27 " ideal model delta sigma weight residual 1.241 1.233 0.007 1.03e-02 9.43e+03 5.09e-01 ... (remaining 3878 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.41: 5071 1.41 - 2.81: 139 2.81 - 4.22: 25 4.22 - 5.62: 6 5.62 - 7.03: 2 Bond angle restraints: 5243 Sorted by residual: angle pdb=" N ILE K 305 " pdb=" CA ILE K 305 " pdb=" C ILE K 305 " ideal model delta sigma weight residual 112.80 109.43 3.37 1.15e+00 7.56e-01 8.58e+00 angle pdb=" N GLN K 351 " pdb=" CA GLN K 351 " pdb=" CB GLN K 351 " ideal model delta sigma weight residual 110.22 114.64 -4.42 1.54e+00 4.22e-01 8.24e+00 angle pdb=" N GLU K 164 " pdb=" CA GLU K 164 " pdb=" CB GLU K 164 " ideal model delta sigma weight residual 110.39 114.81 -4.42 1.66e+00 3.63e-01 7.10e+00 angle pdb=" C VAL K 169 " pdb=" CA VAL K 169 " pdb=" CB VAL K 169 " ideal model delta sigma weight residual 112.46 109.49 2.97 1.33e+00 5.65e-01 4.99e+00 angle pdb=" CA LEU K 234 " pdb=" C LEU K 234 " pdb=" N PRO K 235 " ideal model delta sigma weight residual 118.44 121.95 -3.51 1.59e+00 3.96e-01 4.87e+00 ... (remaining 5238 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.94: 2135 15.94 - 31.89: 224 31.89 - 47.83: 48 47.83 - 63.78: 2 63.78 - 79.72: 3 Dihedral angle restraints: 2412 sinusoidal: 934 harmonic: 1478 Sorted by residual: dihedral pdb=" CA GLU K 354 " pdb=" C GLU K 354 " pdb=" N GLU K 355 " pdb=" CA GLU K 355 " ideal model delta harmonic sigma weight residual 180.00 155.33 24.67 0 5.00e+00 4.00e-02 2.43e+01 dihedral pdb=" CA PHE K 219 " pdb=" C PHE K 219 " pdb=" N ILE K 220 " pdb=" CA ILE K 220 " ideal model delta harmonic sigma weight residual -180.00 -163.83 -16.17 0 5.00e+00 4.00e-02 1.05e+01 dihedral pdb=" N LYS K 321 " pdb=" CA LYS K 321 " pdb=" CB LYS K 321 " pdb=" CG LYS K 321 " ideal model delta sinusoidal sigma weight residual -60.00 -112.99 52.99 3 1.50e+01 4.44e-03 9.17e+00 ... (remaining 2409 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 394 0.028 - 0.057: 154 0.057 - 0.085: 49 0.085 - 0.113: 31 0.113 - 0.142: 10 Chirality restraints: 638 Sorted by residual: chirality pdb=" CA GLU K 164 " pdb=" N GLU K 164 " pdb=" C GLU K 164 " pdb=" CB GLU K 164 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 5.01e-01 chirality pdb=" CA GLN K 72 " pdb=" N GLN K 72 " pdb=" C GLN K 72 " pdb=" CB GLN K 72 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.54e-01 chirality pdb=" CA GLU K 354 " pdb=" N GLU K 354 " pdb=" C GLU K 354 " pdb=" CB GLU K 354 " both_signs ideal model delta sigma weight residual False 2.51 2.39 0.12 2.00e-01 2.50e+01 3.80e-01 ... (remaining 635 not shown) Planarity restraints: 687 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS K 160 " 0.007 2.00e-02 2.50e+03 1.40e-02 1.95e+00 pdb=" C LYS K 160 " -0.024 2.00e-02 2.50e+03 pdb=" O LYS K 160 " 0.009 2.00e-02 2.50e+03 pdb=" N LEU K 161 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU K 161 " 0.006 2.00e-02 2.50e+03 1.23e-02 1.51e+00 pdb=" C LEU K 161 " -0.021 2.00e-02 2.50e+03 pdb=" O LEU K 161 " 0.008 2.00e-02 2.50e+03 pdb=" N ILE K 162 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU K 234 " -0.018 5.00e-02 4.00e+02 2.74e-02 1.20e+00 pdb=" N PRO K 235 " 0.047 5.00e-02 4.00e+02 pdb=" CA PRO K 235 " -0.014 5.00e-02 4.00e+02 pdb=" CD PRO K 235 " -0.016 5.00e-02 4.00e+02 ... (remaining 684 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 65 2.67 - 3.23: 3838 3.23 - 3.78: 6356 3.78 - 4.34: 7900 4.34 - 4.90: 13141 Nonbonded interactions: 31300 Sorted by model distance: nonbonded pdb=" OG1 THR K 385 " pdb=" OE1 GLU K 388 " model vdw 2.109 3.040 nonbonded pdb=" O VAL K 147 " pdb=" OG SER K 151 " model vdw 2.152 3.040 nonbonded pdb=" O GLY K 173 " pdb=" NH2 ARG K 404 " model vdw 2.175 3.120 nonbonded pdb=" OG SER K 228 " pdb=" OE2 GLU K 255 " model vdw 2.224 3.040 nonbonded pdb=" OG1 THR K 296 " pdb=" O GLN K 319 " model vdw 2.249 3.040 ... (remaining 31295 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 1.490 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: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 13.230 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:2.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8205 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 : 0.003 0.042 3883 Z= 0.193 Angle : 0.578 7.027 5243 Z= 0.344 Chirality : 0.041 0.142 638 Planarity : 0.003 0.027 687 Dihedral : 13.124 79.720 1464 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 10.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 0.00 % Allowed : 0.50 % Favored : 99.50 % 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: 1.37 (0.36), residues: 522 helix: 1.78 (0.30), residues: 295 sheet: 0.83 (0.65), residues: 70 loop : -0.72 (0.43), residues: 157 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.000 0.000 HIS K 401 PHE 0.010 0.001 PHE K 195 TYR 0.006 0.001 TYR K 478 ARG 0.002 0.000 ARG K 322 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 50 time to evaluate : 0.456 Fit side-chains revert: symmetry clash REVERT: K 61 GLU cc_start: 0.4353 (pp20) cc_final: 0.3516 (pt0) outliers start: 0 outliers final: 0 residues processed: 50 average time/residue: 0.1385 time to fit residues: 9.1803 Evaluate side-chains 37 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 37 time to evaluate : 0.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 43 optimal weight: 4.9990 chunk 39 optimal weight: 9.9990 chunk 21 optimal weight: 0.5980 chunk 13 optimal weight: 9.9990 chunk 26 optimal weight: 8.9990 chunk 40 optimal weight: 6.9990 chunk 15 optimal weight: 7.9990 chunk 24 optimal weight: 20.0000 chunk 30 optimal weight: 1.9990 chunk 47 optimal weight: 9.9990 chunk 14 optimal weight: 5.9990 overall best weight: 4.1188 ------------------------------------------------------------------------------- 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 = 0.3906 r_free = 0.3906 target = 0.097811 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.069425 restraints weight = 11476.038| |-----------------------------------------------------------------------------| r_work (start): 0.3284 rms_B_bonded: 2.77 r_work: 0.3174 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.3174 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8456 moved from start: 0.1226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 3883 Z= 0.289 Angle : 0.630 10.790 5243 Z= 0.329 Chirality : 0.043 0.147 638 Planarity : 0.004 0.046 687 Dihedral : 4.144 19.686 552 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 11.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 1.49 % Allowed : 9.41 % Favored : 89.11 % 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: 1.34 (0.35), residues: 522 helix: 1.83 (0.30), residues: 297 sheet: 0.81 (0.62), residues: 70 loop : -0.92 (0.42), residues: 155 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.001 HIS K 401 PHE 0.016 0.002 PHE K 195 TYR 0.006 0.001 TYR K 478 ARG 0.004 0.000 ARG K 404 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 36 time to evaluate : 0.606 Fit side-chains REVERT: K 61 GLU cc_start: 0.4917 (pp20) cc_final: 0.4022 (pt0) outliers start: 6 outliers final: 1 residues processed: 41 average time/residue: 0.1545 time to fit residues: 8.4785 Evaluate side-chains 34 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 33 time to evaluate : 0.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 281 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 42 optimal weight: 3.9990 chunk 14 optimal weight: 9.9990 chunk 3 optimal weight: 9.9990 chunk 25 optimal weight: 30.0000 chunk 17 optimal weight: 20.0000 chunk 2 optimal weight: 5.9990 chunk 27 optimal weight: 0.4980 chunk 22 optimal weight: 7.9990 chunk 36 optimal weight: 20.0000 chunk 35 optimal weight: 8.9990 chunk 19 optimal weight: 8.9990 overall best weight: 5.4988 ------------------------------------------------------------------------------- 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 = 0.3870 r_free = 0.3870 target = 0.096504 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.068025 restraints weight = 11598.163| |-----------------------------------------------------------------------------| r_work (start): 0.3240 rms_B_bonded: 2.84 r_work: 0.3129 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8531 moved from start: 0.1791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 3883 Z= 0.343 Angle : 0.623 9.617 5243 Z= 0.325 Chirality : 0.043 0.151 638 Planarity : 0.004 0.039 687 Dihedral : 4.220 17.231 552 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 10.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.15 % Favored : 98.85 % Rotamer: Outliers : 2.72 % Allowed : 10.40 % Favored : 86.88 % 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: 1.21 (0.35), residues: 522 helix: 1.75 (0.29), residues: 297 sheet: 0.68 (0.62), residues: 70 loop : -1.00 (0.42), residues: 155 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.001 HIS K 401 PHE 0.013 0.002 PHE K 195 TYR 0.009 0.001 TYR K 506 ARG 0.004 0.000 ARG K 404 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 36 time to evaluate : 0.415 Fit side-chains revert: symmetry clash REVERT: K 61 GLU cc_start: 0.5599 (pp20) cc_final: 0.4956 (pp20) REVERT: K 351 GLN cc_start: 0.8494 (OUTLIER) cc_final: 0.7752 (pp30) outliers start: 11 outliers final: 6 residues processed: 44 average time/residue: 0.1617 time to fit residues: 9.1230 Evaluate side-chains 40 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 33 time to evaluate : 0.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 60 ILE Chi-restraints excluded: chain K residue 73 MET Chi-restraints excluded: chain K residue 234 LEU Chi-restraints excluded: chain K residue 281 PHE Chi-restraints excluded: chain K residue 351 GLN Chi-restraints excluded: chain K residue 355 GLU Chi-restraints excluded: chain K residue 401 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 21 optimal weight: 3.9990 chunk 26 optimal weight: 20.0000 chunk 41 optimal weight: 0.8980 chunk 37 optimal weight: 20.0000 chunk 50 optimal weight: 2.9990 chunk 34 optimal weight: 50.0000 chunk 35 optimal weight: 30.0000 chunk 25 optimal weight: 5.9990 chunk 14 optimal weight: 10.0000 chunk 22 optimal weight: 9.9990 chunk 10 optimal weight: 3.9990 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 72 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.097050 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.068946 restraints weight = 11701.041| |-----------------------------------------------------------------------------| r_work (start): 0.3256 rms_B_bonded: 2.85 r_work: 0.3146 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8506 moved from start: 0.1944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 3883 Z= 0.250 Angle : 0.577 10.429 5243 Z= 0.296 Chirality : 0.041 0.138 638 Planarity : 0.003 0.034 687 Dihedral : 4.105 16.992 552 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 10.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.77 % Favored : 99.23 % Rotamer: Outliers : 2.23 % Allowed : 12.13 % Favored : 85.64 % 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: 1.37 (0.35), residues: 522 helix: 1.91 (0.28), residues: 297 sheet: 0.70 (0.62), residues: 70 loop : -0.97 (0.42), residues: 155 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.001 HIS K 401 PHE 0.014 0.002 PHE K 195 TYR 0.008 0.001 TYR K 478 ARG 0.003 0.000 ARG K 404 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 33 time to evaluate : 0.459 Fit side-chains REVERT: K 61 GLU cc_start: 0.5499 (pp20) cc_final: 0.4410 (pt0) REVERT: K 267 MET cc_start: 0.5808 (mmt) cc_final: 0.5523 (mmt) REVERT: K 310 GLU cc_start: 0.6346 (pp20) cc_final: 0.6142 (pm20) REVERT: K 351 GLN cc_start: 0.8466 (OUTLIER) cc_final: 0.8165 (pm20) outliers start: 9 outliers final: 4 residues processed: 41 average time/residue: 0.1523 time to fit residues: 8.2647 Evaluate side-chains 36 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 31 time to evaluate : 0.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 60 ILE Chi-restraints excluded: chain K residue 175 ILE Chi-restraints excluded: chain K residue 281 PHE Chi-restraints excluded: chain K residue 351 GLN Chi-restraints excluded: chain K residue 401 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 41 optimal weight: 2.9990 chunk 32 optimal weight: 5.9990 chunk 1 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 chunk 36 optimal weight: 7.9990 chunk 6 optimal weight: 1.9990 chunk 15 optimal weight: 0.4980 chunk 18 optimal weight: 20.0000 chunk 45 optimal weight: 0.9990 chunk 2 optimal weight: 3.9990 chunk 17 optimal weight: 8.9990 overall best weight: 1.8988 ------------------------------------------------------------------------------- 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 = 0.3892 r_free = 0.3892 target = 0.097759 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.069850 restraints weight = 11905.253| |-----------------------------------------------------------------------------| r_work (start): 0.3282 rms_B_bonded: 2.90 r_work: 0.3174 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3174 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8472 moved from start: 0.2012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3883 Z= 0.177 Angle : 0.563 10.818 5243 Z= 0.283 Chirality : 0.040 0.145 638 Planarity : 0.003 0.028 687 Dihedral : 3.972 16.086 552 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.57 % Favored : 99.43 % Rotamer: Outliers : 3.22 % Allowed : 12.13 % Favored : 84.65 % 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: 1.59 (0.35), residues: 522 helix: 2.11 (0.29), residues: 297 sheet: 0.98 (0.64), residues: 64 loop : -0.96 (0.43), residues: 161 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS K 401 PHE 0.015 0.002 PHE K 195 TYR 0.012 0.001 TYR K 506 ARG 0.003 0.000 ARG K 404 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 36 time to evaluate : 0.469 Fit side-chains revert: symmetry clash REVERT: K 61 GLU cc_start: 0.5439 (pp20) cc_final: 0.4329 (pt0) REVERT: K 267 MET cc_start: 0.5824 (mmt) cc_final: 0.5516 (mmt) REVERT: K 351 GLN cc_start: 0.8478 (OUTLIER) cc_final: 0.7966 (pm20) outliers start: 13 outliers final: 6 residues processed: 47 average time/residue: 0.1701 time to fit residues: 10.1836 Evaluate side-chains 39 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 32 time to evaluate : 0.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 72 GLN Chi-restraints excluded: chain K residue 175 ILE Chi-restraints excluded: chain K residue 247 LEU Chi-restraints excluded: chain K residue 281 PHE Chi-restraints excluded: chain K residue 351 GLN Chi-restraints excluded: chain K residue 401 HIS Chi-restraints excluded: chain K residue 411 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 8 optimal weight: 10.0000 chunk 45 optimal weight: 1.9990 chunk 14 optimal weight: 9.9990 chunk 39 optimal weight: 9.9990 chunk 46 optimal weight: 0.9980 chunk 42 optimal weight: 3.9990 chunk 4 optimal weight: 9.9990 chunk 49 optimal weight: 5.9990 chunk 29 optimal weight: 2.9990 chunk 24 optimal weight: 0.0670 chunk 38 optimal weight: 20.0000 overall best weight: 2.0124 ------------------------------------------------------------------------------- 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 = 0.3894 r_free = 0.3894 target = 0.097862 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.070097 restraints weight = 11664.849| |-----------------------------------------------------------------------------| r_work (start): 0.3287 rms_B_bonded: 2.86 r_work: 0.3177 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3177 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8473 moved from start: 0.2158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3883 Z= 0.182 Angle : 0.584 12.632 5243 Z= 0.289 Chirality : 0.040 0.138 638 Planarity : 0.003 0.019 687 Dihedral : 3.936 17.018 552 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 10.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.57 % Favored : 99.43 % Rotamer: Outliers : 2.48 % Allowed : 13.61 % Favored : 83.91 % 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: 1.66 (0.36), residues: 522 helix: 2.17 (0.29), residues: 297 sheet: 0.59 (0.63), residues: 70 loop : -0.77 (0.45), residues: 155 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.000 0.000 HIS K 401 PHE 0.015 0.002 PHE K 195 TYR 0.009 0.001 TYR K 476 ARG 0.003 0.000 ARG K 404 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 33 time to evaluate : 0.444 Fit side-chains revert: symmetry clash REVERT: K 61 GLU cc_start: 0.5376 (pp20) cc_final: 0.4245 (pt0) REVERT: K 267 MET cc_start: 0.5880 (mmt) cc_final: 0.5581 (mmt) REVERT: K 351 GLN cc_start: 0.8445 (OUTLIER) cc_final: 0.8167 (pm20) outliers start: 10 outliers final: 7 residues processed: 42 average time/residue: 0.1541 time to fit residues: 8.6261 Evaluate side-chains 38 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 30 time to evaluate : 0.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 72 GLN Chi-restraints excluded: chain K residue 175 ILE Chi-restraints excluded: chain K residue 247 LEU Chi-restraints excluded: chain K residue 281 PHE Chi-restraints excluded: chain K residue 351 GLN Chi-restraints excluded: chain K residue 388 GLU Chi-restraints excluded: chain K residue 401 HIS Chi-restraints excluded: chain K residue 411 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 38 optimal weight: 10.0000 chunk 19 optimal weight: 20.0000 chunk 20 optimal weight: 8.9990 chunk 33 optimal weight: 20.0000 chunk 46 optimal weight: 1.9990 chunk 50 optimal weight: 3.9990 chunk 23 optimal weight: 20.0000 chunk 37 optimal weight: 10.0000 chunk 48 optimal weight: 5.9990 chunk 51 optimal weight: 6.9990 chunk 12 optimal weight: 0.8980 overall best weight: 3.9788 ------------------------------------------------------------------------------- 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 = 0.3868 r_free = 0.3868 target = 0.096592 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.068544 restraints weight = 11817.837| |-----------------------------------------------------------------------------| r_work (start): 0.3251 rms_B_bonded: 2.89 r_work: 0.3142 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3142 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8515 moved from start: 0.2333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 3883 Z= 0.273 Angle : 0.617 11.410 5243 Z= 0.310 Chirality : 0.042 0.167 638 Planarity : 0.003 0.021 687 Dihedral : 4.042 18.082 552 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 11.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.15 % Favored : 98.85 % Rotamer: Outliers : 2.72 % Allowed : 14.60 % Favored : 82.67 % 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: 1.51 (0.35), residues: 522 helix: 2.07 (0.29), residues: 297 sheet: 0.47 (0.63), residues: 70 loop : -0.86 (0.44), residues: 155 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.001 HIS K 401 PHE 0.014 0.002 PHE K 195 TYR 0.008 0.001 TYR K 476 ARG 0.002 0.000 ARG K 452 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 34 time to evaluate : 0.422 Fit side-chains revert: symmetry clash REVERT: K 61 GLU cc_start: 0.5362 (pp20) cc_final: 0.4366 (pt0) REVERT: K 267 MET cc_start: 0.5907 (mmt) cc_final: 0.5610 (mmt) REVERT: K 351 GLN cc_start: 0.8427 (OUTLIER) cc_final: 0.8186 (pm20) outliers start: 11 outliers final: 9 residues processed: 43 average time/residue: 0.1431 time to fit residues: 8.1943 Evaluate side-chains 42 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 32 time to evaluate : 0.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 72 GLN Chi-restraints excluded: chain K residue 73 MET Chi-restraints excluded: chain K residue 234 LEU Chi-restraints excluded: chain K residue 247 LEU Chi-restraints excluded: chain K residue 281 PHE Chi-restraints excluded: chain K residue 342 ILE Chi-restraints excluded: chain K residue 351 GLN Chi-restraints excluded: chain K residue 388 GLU Chi-restraints excluded: chain K residue 401 HIS Chi-restraints excluded: chain K residue 411 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 8 optimal weight: 2.9990 chunk 25 optimal weight: 3.9990 chunk 38 optimal weight: 1.9990 chunk 51 optimal weight: 6.9990 chunk 32 optimal weight: 7.9990 chunk 30 optimal weight: 0.0770 chunk 49 optimal weight: 2.9990 chunk 44 optimal weight: 0.8980 chunk 12 optimal weight: 3.9990 chunk 48 optimal weight: 6.9990 chunk 46 optimal weight: 0.9990 overall best weight: 1.3944 ------------------------------------------------------------------------------- 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 = 0.3900 r_free = 0.3900 target = 0.098337 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.070642 restraints weight = 11828.076| |-----------------------------------------------------------------------------| r_work (start): 0.3298 rms_B_bonded: 2.91 r_work: 0.3187 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8464 moved from start: 0.2348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3883 Z= 0.170 Angle : 0.581 11.660 5243 Z= 0.288 Chirality : 0.041 0.152 638 Planarity : 0.002 0.020 687 Dihedral : 3.894 20.246 552 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.38 % Favored : 99.62 % Rotamer: Outliers : 3.71 % Allowed : 13.86 % Favored : 82.43 % 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: 1.74 (0.36), residues: 522 helix: 2.27 (0.29), residues: 297 sheet: 0.53 (0.64), residues: 70 loop : -0.80 (0.44), residues: 155 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS K 401 PHE 0.015 0.002 PHE K 195 TYR 0.010 0.001 TYR K 476 ARG 0.001 0.000 ARG K 445 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 34 time to evaluate : 0.443 Fit side-chains revert: symmetry clash REVERT: K 61 GLU cc_start: 0.5149 (pp20) cc_final: 0.4123 (pt0) REVERT: K 72 GLN cc_start: 0.8719 (OUTLIER) cc_final: 0.8328 (mp-120) REVERT: K 267 MET cc_start: 0.5824 (mmt) cc_final: 0.5531 (mmt) REVERT: K 351 GLN cc_start: 0.8439 (OUTLIER) cc_final: 0.8174 (pm20) outliers start: 15 outliers final: 9 residues processed: 46 average time/residue: 0.1349 time to fit residues: 8.2296 Evaluate side-chains 44 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 33 time to evaluate : 0.526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 39 VAL Chi-restraints excluded: chain K residue 72 GLN Chi-restraints excluded: chain K residue 175 ILE Chi-restraints excluded: chain K residue 232 GLU Chi-restraints excluded: chain K residue 234 LEU Chi-restraints excluded: chain K residue 247 LEU Chi-restraints excluded: chain K residue 281 PHE Chi-restraints excluded: chain K residue 351 GLN Chi-restraints excluded: chain K residue 388 GLU Chi-restraints excluded: chain K residue 411 VAL Chi-restraints excluded: chain K residue 514 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 3 optimal weight: 0.9980 chunk 41 optimal weight: 6.9990 chunk 20 optimal weight: 4.9990 chunk 19 optimal weight: 20.0000 chunk 15 optimal weight: 0.8980 chunk 31 optimal weight: 7.9990 chunk 39 optimal weight: 5.9990 chunk 36 optimal weight: 8.9990 chunk 10 optimal weight: 0.9990 chunk 21 optimal weight: 5.9990 chunk 47 optimal weight: 7.9990 overall best weight: 2.7786 ------------------------------------------------------------------------------- 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 = 0.3889 r_free = 0.3889 target = 0.097951 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.069990 restraints weight = 11919.918| |-----------------------------------------------------------------------------| r_work (start): 0.3277 rms_B_bonded: 2.94 r_work: 0.3163 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3163 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8494 moved from start: 0.2373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3883 Z= 0.216 Angle : 0.619 11.254 5243 Z= 0.307 Chirality : 0.042 0.151 638 Planarity : 0.003 0.020 687 Dihedral : 3.958 20.324 552 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 11.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.96 % Favored : 99.04 % Rotamer: Outliers : 3.71 % Allowed : 14.36 % Favored : 81.93 % 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: 1.68 (0.36), residues: 522 helix: 2.23 (0.29), residues: 297 sheet: 0.41 (0.63), residues: 70 loop : -0.78 (0.45), residues: 155 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.001 HIS K 401 PHE 0.012 0.002 PHE K 195 TYR 0.009 0.001 TYR K 476 ARG 0.001 0.000 ARG K 501 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 32 time to evaluate : 0.444 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: K 61 GLU cc_start: 0.5285 (pp20) cc_final: 0.4275 (pt0) REVERT: K 267 MET cc_start: 0.5812 (mmt) cc_final: 0.5545 (mmt) REVERT: K 351 GLN cc_start: 0.8437 (OUTLIER) cc_final: 0.8105 (pm20) outliers start: 15 outliers final: 11 residues processed: 44 average time/residue: 0.1463 time to fit residues: 8.5655 Evaluate side-chains 42 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 30 time to evaluate : 0.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 16 MET Chi-restraints excluded: chain K residue 39 VAL Chi-restraints excluded: chain K residue 72 GLN Chi-restraints excluded: chain K residue 232 GLU Chi-restraints excluded: chain K residue 234 LEU Chi-restraints excluded: chain K residue 247 LEU Chi-restraints excluded: chain K residue 281 PHE Chi-restraints excluded: chain K residue 351 GLN Chi-restraints excluded: chain K residue 388 GLU Chi-restraints excluded: chain K residue 401 HIS Chi-restraints excluded: chain K residue 411 VAL Chi-restraints excluded: chain K residue 514 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/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-5571/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/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-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/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-5571/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-5571/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-5571/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-5571/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-5571/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-5571/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-5571/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-5571/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/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-5571/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-5571/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-5571/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-5571/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: 51.021 > 50: distance: 60 - 90: 6.889 distance: 66 - 101: 8.166 distance: 72 - 82: 15.600 distance: 73 - 110: 6.297 distance: 82 - 83: 5.224 distance: 83 - 84: 7.146 distance: 83 - 86: 4.876 distance: 84 - 85: 16.302 distance: 84 - 90: 6.391 distance: 85 - 119: 17.871 distance: 86 - 87: 10.026 distance: 87 - 88: 9.764 distance: 87 - 89: 10.788 distance: 90 - 91: 6.114 distance: 91 - 92: 8.304 distance: 92 - 93: 14.129 distance: 92 - 101: 12.269 distance: 93 - 127: 20.377 distance: 94 - 95: 5.702 distance: 95 - 96: 11.858 distance: 96 - 97: 5.932 distance: 97 - 98: 3.045 distance: 98 - 99: 4.071 distance: 98 - 100: 11.485 distance: 101 - 102: 7.177 distance: 102 - 103: 3.475 distance: 102 - 105: 6.804 distance: 103 - 104: 7.072 distance: 103 - 110: 4.796 distance: 104 - 136: 15.735 distance: 105 - 106: 7.659 distance: 106 - 107: 9.831 distance: 107 - 108: 5.608 distance: 107 - 109: 7.742 distance: 110 - 111: 5.063 distance: 111 - 112: 3.064 distance: 111 - 114: 4.611 distance: 112 - 113: 30.228 distance: 112 - 119: 6.545 distance: 113 - 145: 43.398 distance: 114 - 115: 8.132 distance: 115 - 116: 4.516 distance: 116 - 117: 14.802 distance: 117 - 118: 7.017 distance: 119 - 120: 3.448 distance: 120 - 121: 12.273 distance: 120 - 123: 9.621 distance: 121 - 122: 10.310 distance: 121 - 127: 18.250 distance: 122 - 156: 28.671 distance: 123 - 124: 9.901 distance: 124 - 125: 5.585 distance: 124 - 126: 28.862 distance: 127 - 128: 7.295 distance: 128 - 129: 9.677 distance: 128 - 131: 10.090 distance: 129 - 130: 13.773 distance: 129 - 136: 10.173 distance: 130 - 163: 32.623 distance: 131 - 132: 9.418 distance: 132 - 133: 10.252 distance: 133 - 134: 8.959 distance: 133 - 135: 24.822 distance: 136 - 137: 11.152 distance: 137 - 138: 13.931 distance: 137 - 140: 11.248 distance: 138 - 139: 15.136 distance: 138 - 145: 26.827 distance: 139 - 168: 18.228 distance: 140 - 141: 11.437 distance: 141 - 142: 13.531 distance: 142 - 144: 11.452 distance: 145 - 146: 26.874 distance: 146 - 147: 24.620 distance: 146 - 149: 19.696 distance: 147 - 148: 19.806 distance: 147 - 156: 8.061 distance: 148 - 174: 18.463 distance: 149 - 150: 21.639 distance: 150 - 151: 23.940 distance: 151 - 152: 22.367 distance: 152 - 153: 15.910 distance: 153 - 154: 20.551 distance: 153 - 155: 23.576 distance: 156 - 157: 9.591 distance: 157 - 158: 8.402 distance: 157 - 160: 6.454 distance: 158 - 159: 11.591 distance: 158 - 163: 10.806 distance: 159 - 181: 14.653 distance: 160 - 161: 11.323 distance: 160 - 162: 21.199 distance: 163 - 164: 6.268 distance: 164 - 165: 6.535 distance: 164 - 167: 7.779 distance: 165 - 166: 6.984 distance: 165 - 168: 14.188 distance: 166 - 186: 21.693