Starting phenix.real_space_refine on Mon Feb 10 22:24:24 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8z7y_39832/02_2025/8z7y_39832.cif Found real_map, /net/cci-nas-00/data/ceres_data/8z7y_39832/02_2025/8z7y_39832.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.02 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8z7y_39832/02_2025/8z7y_39832.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8z7y_39832/02_2025/8z7y_39832.map" model { file = "/net/cci-nas-00/data/ceres_data/8z7y_39832/02_2025/8z7y_39832.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8z7y_39832/02_2025/8z7y_39832.cif" } resolution = 3.02 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= 0.157 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 16 5.16 5 C 2082 2.51 5 N 463 2.21 5 O 522 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 3083 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3046 Number of conformers: 1 Conformer: "" Number of residues, atoms: 382, 3046 Classifications: {'peptide': 382} Link IDs: {'PTRANS': 13, 'TRANS': 368} Chain breaks: 1 Chain: "A" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 37 Unusual residues: {'2TA': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.72, per 1000 atoms: 0.88 Number of scatterers: 3083 At special positions: 0 Unit cell: (82.948, 58.716, 69.9, 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 16 16.00 O 522 8.00 N 463 7.00 C 2082 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: 0.96 Conformation dependent library (CDL) restraints added in 355.9 milliseconds 756 Ramachandran restraints generated. 378 Oldfield, 0 Emsley, 378 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 724 Finding SS restraints... Secondary structure from input PDB file: 15 helices and 0 sheets defined 84.0% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.26 Creating SS restraints... Processing helix chain 'A' and resid 13 through 28 removed outlier: 3.647A pdb=" N VAL A 17 " --> pdb=" O ILE A 13 " (cutoff:3.500A) Processing helix chain 'A' and resid 35 through 40 Processing helix chain 'A' and resid 47 through 54 Processing helix chain 'A' and resid 56 through 77 removed outlier: 4.098A pdb=" N THR A 60 " --> pdb=" O PHE A 56 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N TYR A 61 " --> pdb=" O PRO A 57 " (cutoff:3.500A) removed outlier: 4.923A pdb=" N LEU A 68 " --> pdb=" O LEU A 64 " (cutoff:3.500A) Proline residue: A 69 - end of helix removed outlier: 3.716A pdb=" N ASP A 75 " --> pdb=" O PHE A 71 " (cutoff:3.500A) Processing helix chain 'A' and resid 79 through 99 removed outlier: 3.645A pdb=" N ILE A 83 " --> pdb=" O TYR A 79 " (cutoff:3.500A) Processing helix chain 'A' and resid 102 through 131 removed outlier: 4.523A pdb=" N VAL A 121 " --> pdb=" O THR A 117 " (cutoff:3.500A) removed outlier: 5.340A pdb=" N ALA A 122 " --> pdb=" O ALA A 118 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N TYR A 123 " --> pdb=" O ALA A 119 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N TYR A 124 " --> pdb=" O GLU A 120 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N ILE A 127 " --> pdb=" O TYR A 123 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N TYR A 128 " --> pdb=" O TYR A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 136 through 166 removed outlier: 3.573A pdb=" N ASN A 166 " --> pdb=" O VAL A 162 " (cutoff:3.500A) Processing helix chain 'A' and resid 168 through 189 removed outlier: 4.254A pdb=" N PHE A 189 " --> pdb=" O LEU A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 307 removed outlier: 4.240A pdb=" N TRP A 281 " --> pdb=" O ARG A 277 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N TYR A 298 " --> pdb=" O GLN A 294 " (cutoff:3.500A) removed outlier: 4.858A pdb=" N GLN A 300 " --> pdb=" O LEU A 296 " (cutoff:3.500A) removed outlier: 5.757A pdb=" N ILE A 301 " --> pdb=" O ASN A 297 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LYS A 306 " --> pdb=" O LEU A 302 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ALA A 307 " --> pdb=" O TRP A 303 " (cutoff:3.500A) Processing helix chain 'A' and resid 315 through 337 removed outlier: 4.015A pdb=" N GLY A 335 " --> pdb=" O ALA A 331 " (cutoff:3.500A) Processing helix chain 'A' and resid 344 through 366 Processing helix chain 'A' and resid 368 through 396 Processing helix chain 'A' and resid 399 through 426 removed outlier: 3.987A pdb=" N ALA A 404 " --> pdb=" O VAL A 400 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N LEU A 405 " --> pdb=" O GLU A 401 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N ILE A 409 " --> pdb=" O LEU A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 434 through 456 removed outlier: 3.791A pdb=" N PHE A 439 " --> pdb=" O VAL A 435 " (cutoff:3.500A) removed outlier: 5.508A pdb=" N LEU A 440 " --> pdb=" O SER A 436 " (cutoff:3.500A) Processing helix chain 'A' and resid 458 through 465 removed outlier: 4.276A pdb=" N TYR A 462 " --> pdb=" O MET A 458 " (cutoff:3.500A) 231 hydrogen bonds defined for protein. 693 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: 0.83 Time building geometry restraints manager: 1.01 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 440 1.30 - 1.43: 942 1.43 - 1.56: 1763 1.56 - 1.69: 2 1.69 - 1.81: 29 Bond restraints: 3176 Sorted by residual: bond pdb=" CAO 2TA A 501 " pdb=" NAP 2TA A 501 " ideal model delta sigma weight residual 1.444 1.173 0.271 2.00e-02 2.50e+03 1.83e+02 bond pdb=" CAS 2TA A 501 " pdb=" CAT 2TA A 501 " ideal model delta sigma weight residual 1.532 1.323 0.209 2.00e-02 2.50e+03 1.09e+02 bond pdb=" CAQ 2TA A 501 " pdb=" NAP 2TA A 501 " ideal model delta sigma weight residual 1.454 1.256 0.198 2.00e-02 2.50e+03 9.77e+01 bond pdb=" C2 2TA A 501 " pdb=" N1 2TA A 501 " ideal model delta sigma weight residual 1.322 1.487 -0.165 2.00e-02 2.50e+03 6.79e+01 bond pdb=" CAY 2TA A 501 " pdb=" CAZ 2TA A 501 " ideal model delta sigma weight residual 1.386 1.536 -0.150 2.00e-02 2.50e+03 5.60e+01 ... (remaining 3171 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.25: 4301 3.25 - 6.50: 36 6.50 - 9.75: 0 9.75 - 13.00: 1 13.00 - 16.25: 2 Bond angle restraints: 4340 Sorted by residual: angle pdb=" OBJ 2TA A 501 " pdb=" SBD 2TA A 501 " pdb=" OBK 2TA A 501 " ideal model delta sigma weight residual 118.13 101.88 16.25 3.00e+00 1.11e-01 2.94e+01 angle pdb=" C4 2TA A 501 " pdb=" NAW 2TA A 501 " pdb=" CAX 2TA A 501 " ideal model delta sigma weight residual 131.24 116.51 14.73 3.00e+00 1.11e-01 2.41e+01 angle pdb=" C2 2TA A 501 " pdb=" NAF 2TA A 501 " pdb=" CAG 2TA A 501 " ideal model delta sigma weight residual 131.32 119.61 11.71 3.00e+00 1.11e-01 1.52e+01 angle pdb=" N PRO A 191 " pdb=" CA PRO A 191 " pdb=" CB PRO A 191 " ideal model delta sigma weight residual 103.35 105.90 -2.55 8.70e-01 1.32e+00 8.57e+00 angle pdb=" N TYR A 126 " pdb=" CA TYR A 126 " pdb=" C TYR A 126 " ideal model delta sigma weight residual 111.28 108.30 2.98 1.09e+00 8.42e-01 7.50e+00 ... (remaining 4335 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.64: 1749 33.64 - 67.28: 43 67.28 - 100.92: 5 100.92 - 134.56: 1 134.56 - 168.19: 1 Dihedral angle restraints: 1799 sinusoidal: 665 harmonic: 1134 Sorted by residual: dihedral pdb=" CA ARG A 78 " pdb=" C ARG A 78 " pdb=" N TYR A 79 " pdb=" CA TYR A 79 " ideal model delta harmonic sigma weight residual 180.00 156.87 23.13 0 5.00e+00 4.00e-02 2.14e+01 dihedral pdb=" CAG 2TA A 501 " pdb=" C2 2TA A 501 " pdb=" NAF 2TA A 501 " pdb=" N1 2TA A 501 " ideal model delta sinusoidal sigma weight residual -0.72 -168.91 168.19 1 3.00e+01 1.11e-03 2.11e+01 dihedral pdb=" CAI 2TA A 501 " pdb=" CAJ 2TA A 501 " pdb=" OAM 2TA A 501 " pdb=" CAN 2TA A 501 " ideal model delta sinusoidal sigma weight residual -1.36 -123.50 122.14 1 3.00e+01 1.11e-03 1.63e+01 ... (remaining 1796 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 381 0.047 - 0.095: 96 0.095 - 0.142: 18 0.142 - 0.190: 2 0.190 - 0.237: 1 Chirality restraints: 498 Sorted by residual: chirality pdb=" CB VAL A 77 " pdb=" CA VAL A 77 " pdb=" CG1 VAL A 77 " pdb=" CG2 VAL A 77 " both_signs ideal model delta sigma weight residual False -2.63 -2.39 -0.24 2.00e-01 2.50e+01 1.41e+00 chirality pdb=" CB VAL A 109 " pdb=" CA VAL A 109 " pdb=" CG1 VAL A 109 " pdb=" CG2 VAL A 109 " both_signs ideal model delta sigma weight residual False -2.63 -2.47 -0.16 2.00e-01 2.50e+01 6.68e-01 chirality pdb=" CA PHE A 56 " pdb=" N PHE A 56 " pdb=" C PHE A 56 " pdb=" CB PHE A 56 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 5.15e-01 ... (remaining 495 not shown) Planarity restraints: 516 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 56 " -0.009 2.00e-02 2.50e+03 9.40e-03 1.55e+00 pdb=" CG PHE A 56 " 0.022 2.00e-02 2.50e+03 pdb=" CD1 PHE A 56 " -0.006 2.00e-02 2.50e+03 pdb=" CD2 PHE A 56 " -0.003 2.00e-02 2.50e+03 pdb=" CE1 PHE A 56 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE A 56 " -0.003 2.00e-02 2.50e+03 pdb=" CZ PHE A 56 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN A 393 " -0.005 2.00e-02 2.50e+03 1.08e-02 1.16e+00 pdb=" CD GLN A 393 " 0.019 2.00e-02 2.50e+03 pdb=" OE1 GLN A 393 " -0.007 2.00e-02 2.50e+03 pdb=" NE2 GLN A 393 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE A 36 " 0.018 5.00e-02 4.00e+02 2.68e-02 1.15e+00 pdb=" N PRO A 37 " -0.046 5.00e-02 4.00e+02 pdb=" CA PRO A 37 " 0.013 5.00e-02 4.00e+02 pdb=" CD PRO A 37 " 0.015 5.00e-02 4.00e+02 ... (remaining 513 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 424 2.75 - 3.29: 3215 3.29 - 3.83: 5427 3.83 - 4.36: 6289 4.36 - 4.90: 10948 Nonbonded interactions: 26303 Sorted by model distance: nonbonded pdb=" O PHE A 25 " pdb=" OG SER A 179 " model vdw 2.215 3.040 nonbonded pdb=" O SER A 26 " pdb=" NH1 ARG A 29 " model vdw 2.246 3.120 nonbonded pdb=" NH1 ARG A 277 " pdb=" OH TYR A 280 " model vdw 2.288 3.120 nonbonded pdb=" O MET A 192 " pdb=" NZ LYS A 194 " model vdw 2.355 3.120 nonbonded pdb=" NE2 GLN A 159 " pdb=" OG SER A 163 " model vdw 2.368 3.120 ... (remaining 26298 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: 1.250 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: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 12.630 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:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6489 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 : 0.013 0.271 3176 Z= 0.781 Angle : 0.799 16.255 4340 Z= 0.388 Chirality : 0.044 0.237 498 Planarity : 0.004 0.027 516 Dihedral : 16.151 168.195 1075 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 10.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: 1.07 (0.44), residues: 378 helix: 1.18 (0.30), residues: 302 sheet: None (None), residues: 0 loop : -1.01 (0.72), residues: 76 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 94 HIS 0.003 0.001 HIS A 200 PHE 0.022 0.002 PHE A 56 TYR 0.012 0.001 TYR A 151 ARG 0.002 0.000 ARG A 78 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 756 Ramachandran restraints generated. 378 Oldfield, 0 Emsley, 378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 756 Ramachandran restraints generated. 378 Oldfield, 0 Emsley, 378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 43 time to evaluate : 0.272 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 43 average time/residue: 0.1031 time to fit residues: 6.1988 Evaluate side-chains 38 residues out of total 327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 38 time to evaluate : 0.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 32 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 15 optimal weight: 0.0870 chunk 9 optimal weight: 0.7980 chunk 19 optimal weight: 3.9990 chunk 29 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 18 optimal weight: 0.0040 chunk 22 optimal weight: 4.9990 chunk 34 optimal weight: 0.0370 chunk 10 optimal weight: 0.7980 overall best weight: 0.3448 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 294 GLN A 300 GLN A 316 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4353 r_free = 0.4353 target = 0.215297 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4151 r_free = 0.4151 target = 0.191943 restraints weight = 3253.931| |-----------------------------------------------------------------------------| r_work (start): 0.4185 rms_B_bonded: 1.54 r_work: 0.4096 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3969 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6591 moved from start: 0.1105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 3176 Z= 0.176 Angle : 0.526 5.266 4340 Z= 0.271 Chirality : 0.040 0.146 498 Planarity : 0.004 0.035 516 Dihedral : 12.232 157.468 434 Min Nonbonded Distance : 2.626 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 0.61 % Allowed : 6.12 % Favored : 93.27 % 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: 1.20 (0.44), residues: 378 helix: 1.26 (0.30), residues: 305 sheet: None (None), residues: 0 loop : -0.99 (0.75), residues: 73 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 94 HIS 0.003 0.001 HIS A 200 PHE 0.012 0.001 PHE A 279 TYR 0.009 0.001 TYR A 38 ARG 0.002 0.000 ARG A 277 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 756 Ramachandran restraints generated. 378 Oldfield, 0 Emsley, 378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 756 Ramachandran restraints generated. 378 Oldfield, 0 Emsley, 378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 42 time to evaluate : 0.332 Fit side-chains REVERT: A 392 PHE cc_start: 0.5762 (m-10) cc_final: 0.5538 (m-80) outliers start: 2 outliers final: 1 residues processed: 43 average time/residue: 0.0981 time to fit residues: 5.9125 Evaluate side-chains 41 residues out of total 327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 40 time to evaluate : 0.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 34 optimal weight: 1.9990 chunk 4 optimal weight: 0.3980 chunk 14 optimal weight: 1.9990 chunk 3 optimal weight: 0.9980 chunk 17 optimal weight: 0.1980 chunk 25 optimal weight: 0.0030 chunk 26 optimal weight: 0.9990 chunk 2 optimal weight: 0.9990 chunk 24 optimal weight: 1.9990 chunk 31 optimal weight: 0.0870 chunk 23 optimal weight: 1.9990 overall best weight: 0.3368 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 300 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4363 r_free = 0.4363 target = 0.216036 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4161 r_free = 0.4161 target = 0.192873 restraints weight = 3146.085| |-----------------------------------------------------------------------------| r_work (start): 0.4145 rms_B_bonded: 1.51 r_work: 0.4052 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3929 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3929 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6590 moved from start: 0.1293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3176 Z= 0.165 Angle : 0.507 5.181 4340 Z= 0.260 Chirality : 0.039 0.130 498 Planarity : 0.004 0.036 516 Dihedral : 10.661 142.949 434 Min Nonbonded Distance : 2.624 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 1.22 % Allowed : 9.48 % Favored : 89.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.40 (0.44), residues: 378 helix: 1.36 (0.30), residues: 307 sheet: None (None), residues: 0 loop : -0.79 (0.79), residues: 71 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 94 HIS 0.003 0.001 HIS A 200 PHE 0.009 0.001 PHE A 56 TYR 0.009 0.001 TYR A 38 ARG 0.002 0.000 ARG A 29 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 756 Ramachandran restraints generated. 378 Oldfield, 0 Emsley, 378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 756 Ramachandran restraints generated. 378 Oldfield, 0 Emsley, 378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 41 time to evaluate : 0.292 Fit side-chains REVERT: A 392 PHE cc_start: 0.5777 (m-10) cc_final: 0.5565 (m-10) outliers start: 4 outliers final: 3 residues processed: 43 average time/residue: 0.0935 time to fit residues: 5.6207 Evaluate side-chains 42 residues out of total 327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 39 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 VAL Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 353 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 3 optimal weight: 1.9990 chunk 21 optimal weight: 0.7980 chunk 1 optimal weight: 1.9990 chunk 16 optimal weight: 0.9980 chunk 23 optimal weight: 0.9980 chunk 27 optimal weight: 0.7980 chunk 25 optimal weight: 0.0970 chunk 4 optimal weight: 0.7980 chunk 29 optimal weight: 0.5980 chunk 28 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 overall best weight: 0.6178 ------------------------------------------------------------------------------- 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 = 0.4295 r_free = 0.4295 target = 0.209497 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4080 r_free = 0.4080 target = 0.185484 restraints weight = 3343.459| |-----------------------------------------------------------------------------| r_work (start): 0.4094 rms_B_bonded: 1.55 r_work: 0.4003 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3875 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3875 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6673 moved from start: 0.1304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3176 Z= 0.223 Angle : 0.564 7.109 4340 Z= 0.285 Chirality : 0.041 0.145 498 Planarity : 0.004 0.038 516 Dihedral : 10.274 137.948 434 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 1.83 % Allowed : 11.62 % Favored : 86.54 % 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: 1.25 (0.43), residues: 378 helix: 1.28 (0.29), residues: 306 sheet: None (None), residues: 0 loop : -0.94 (0.76), residues: 72 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 94 HIS 0.003 0.001 HIS A 200 PHE 0.012 0.001 PHE A 56 TYR 0.010 0.001 TYR A 126 ARG 0.002 0.000 ARG A 78 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 756 Ramachandran restraints generated. 378 Oldfield, 0 Emsley, 378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 756 Ramachandran restraints generated. 378 Oldfield, 0 Emsley, 378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 40 time to evaluate : 0.301 Fit side-chains REVERT: A 97 LEU cc_start: 0.6968 (OUTLIER) cc_final: 0.6547 (mp) outliers start: 6 outliers final: 5 residues processed: 43 average time/residue: 0.0972 time to fit residues: 5.8937 Evaluate side-chains 46 residues out of total 327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 40 time to evaluate : 0.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 VAL Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 353 SER Chi-restraints excluded: chain A residue 421 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 30 optimal weight: 1.9990 chunk 26 optimal weight: 0.9980 chunk 12 optimal weight: 0.4980 chunk 18 optimal weight: 1.9990 chunk 20 optimal weight: 0.6980 chunk 36 optimal weight: 0.9990 chunk 19 optimal weight: 2.9990 chunk 7 optimal weight: 0.7980 chunk 32 optimal weight: 0.9990 chunk 35 optimal weight: 0.9990 chunk 0 optimal weight: 1.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- 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 = 0.4276 r_free = 0.4276 target = 0.206729 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.182867 restraints weight = 3298.932| |-----------------------------------------------------------------------------| r_work (start): 0.4126 rms_B_bonded: 1.52 r_work: 0.4037 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3909 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3909 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6711 moved from start: 0.1505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 3176 Z= 0.264 Angle : 0.606 8.470 4340 Z= 0.302 Chirality : 0.042 0.164 498 Planarity : 0.004 0.038 516 Dihedral : 10.173 135.347 434 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 1.83 % Allowed : 14.07 % Favored : 84.10 % 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: 1.15 (0.43), residues: 378 helix: 1.18 (0.29), residues: 307 sheet: None (None), residues: 0 loop : -0.86 (0.75), residues: 71 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 94 HIS 0.003 0.001 HIS A 200 PHE 0.013 0.002 PHE A 56 TYR 0.011 0.002 TYR A 126 ARG 0.002 0.001 ARG A 277 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 756 Ramachandran restraints generated. 378 Oldfield, 0 Emsley, 378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 756 Ramachandran restraints generated. 378 Oldfield, 0 Emsley, 378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 42 time to evaluate : 0.298 Fit side-chains REVERT: A 396 VAL cc_start: 0.4277 (OUTLIER) cc_final: 0.3771 (m) outliers start: 6 outliers final: 5 residues processed: 45 average time/residue: 0.0944 time to fit residues: 5.9361 Evaluate side-chains 47 residues out of total 327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 41 time to evaluate : 0.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 VAL Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 353 SER Chi-restraints excluded: chain A residue 396 VAL Chi-restraints excluded: chain A residue 421 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 28 optimal weight: 3.9990 chunk 17 optimal weight: 0.6980 chunk 32 optimal weight: 1.9990 chunk 30 optimal weight: 0.5980 chunk 33 optimal weight: 0.1980 chunk 25 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 chunk 21 optimal weight: 0.6980 chunk 12 optimal weight: 2.9990 chunk 7 optimal weight: 0.9980 chunk 4 optimal weight: 0.7980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 300 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4275 r_free = 0.4275 target = 0.207656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.183863 restraints weight = 3359.232| |-----------------------------------------------------------------------------| r_work (start): 0.4060 rms_B_bonded: 1.52 r_work: 0.3969 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3843 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3843 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6698 moved from start: 0.1558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3176 Z= 0.217 Angle : 0.564 7.585 4340 Z= 0.283 Chirality : 0.041 0.171 498 Planarity : 0.004 0.039 516 Dihedral : 10.239 136.430 434 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 3.06 % Allowed : 14.37 % Favored : 82.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.27 (0.43), residues: 378 helix: 1.27 (0.30), residues: 307 sheet: None (None), residues: 0 loop : -0.82 (0.75), residues: 71 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 94 HIS 0.003 0.001 HIS A 200 PHE 0.009 0.001 PHE A 56 TYR 0.010 0.001 TYR A 126 ARG 0.002 0.000 ARG A 429 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 756 Ramachandran restraints generated. 378 Oldfield, 0 Emsley, 378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 756 Ramachandran restraints generated. 378 Oldfield, 0 Emsley, 378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 40 time to evaluate : 0.344 Fit side-chains REVERT: A 97 LEU cc_start: 0.6958 (OUTLIER) cc_final: 0.6597 (mp) REVERT: A 320 GLU cc_start: 0.7087 (tt0) cc_final: 0.6726 (tt0) REVERT: A 396 VAL cc_start: 0.4415 (OUTLIER) cc_final: 0.3923 (m) outliers start: 10 outliers final: 6 residues processed: 47 average time/residue: 0.0943 time to fit residues: 6.2185 Evaluate side-chains 48 residues out of total 327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 40 time to evaluate : 0.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 VAL Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 109 VAL Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 353 SER Chi-restraints excluded: chain A residue 396 VAL Chi-restraints excluded: chain A residue 421 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 10 optimal weight: 0.5980 chunk 18 optimal weight: 0.9980 chunk 33 optimal weight: 0.5980 chunk 28 optimal weight: 2.9990 chunk 21 optimal weight: 0.6980 chunk 29 optimal weight: 0.5980 chunk 35 optimal weight: 0.5980 chunk 16 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 chunk 30 optimal weight: 0.5980 chunk 8 optimal weight: 0.7980 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 = 0.4287 r_free = 0.4287 target = 0.208590 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4072 r_free = 0.4072 target = 0.184413 restraints weight = 3268.200| |-----------------------------------------------------------------------------| r_work (start): 0.4069 rms_B_bonded: 1.53 r_work: 0.3978 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3854 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3854 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6711 moved from start: 0.1632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3176 Z= 0.216 Angle : 0.564 7.111 4340 Z= 0.282 Chirality : 0.040 0.188 498 Planarity : 0.004 0.039 516 Dihedral : 10.258 136.593 434 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 2.45 % Allowed : 14.07 % Favored : 83.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.35 (0.44), residues: 378 helix: 1.32 (0.30), residues: 307 sheet: None (None), residues: 0 loop : -0.77 (0.76), residues: 71 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 94 HIS 0.003 0.001 HIS A 200 PHE 0.008 0.001 PHE A 56 TYR 0.010 0.001 TYR A 126 ARG 0.002 0.000 ARG A 429 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 756 Ramachandran restraints generated. 378 Oldfield, 0 Emsley, 378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 756 Ramachandran restraints generated. 378 Oldfield, 0 Emsley, 378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 41 time to evaluate : 0.280 Fit side-chains REVERT: A 97 LEU cc_start: 0.7063 (OUTLIER) cc_final: 0.6664 (mp) REVERT: A 396 VAL cc_start: 0.4206 (OUTLIER) cc_final: 0.3759 (m) outliers start: 8 outliers final: 6 residues processed: 46 average time/residue: 0.0882 time to fit residues: 5.7027 Evaluate side-chains 46 residues out of total 327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 38 time to evaluate : 0.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 VAL Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 109 VAL Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 353 SER Chi-restraints excluded: chain A residue 396 VAL Chi-restraints excluded: chain A residue 421 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 4 optimal weight: 0.9990 chunk 32 optimal weight: 0.6980 chunk 30 optimal weight: 1.9990 chunk 7 optimal weight: 0.8980 chunk 15 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 chunk 1 optimal weight: 0.8980 chunk 17 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 chunk 9 optimal weight: 0.9980 chunk 10 optimal weight: 0.5980 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 = 0.4283 r_free = 0.4283 target = 0.207105 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.182892 restraints weight = 3327.927| |-----------------------------------------------------------------------------| r_work (start): 0.4051 rms_B_bonded: 1.54 r_work: 0.3957 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3829 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3829 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6735 moved from start: 0.1693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 3176 Z= 0.267 Angle : 0.598 6.696 4340 Z= 0.300 Chirality : 0.042 0.186 498 Planarity : 0.004 0.039 516 Dihedral : 10.172 134.876 434 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 2.45 % Allowed : 14.98 % Favored : 82.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.22 (0.44), residues: 378 helix: 1.22 (0.30), residues: 307 sheet: None (None), residues: 0 loop : -0.80 (0.75), residues: 71 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 94 HIS 0.003 0.001 HIS A 200 PHE 0.011 0.002 PHE A 189 TYR 0.011 0.002 TYR A 126 ARG 0.002 0.001 ARG A 29 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 756 Ramachandran restraints generated. 378 Oldfield, 0 Emsley, 378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 756 Ramachandran restraints generated. 378 Oldfield, 0 Emsley, 378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 42 time to evaluate : 0.314 Fit side-chains REVERT: A 97 LEU cc_start: 0.7105 (OUTLIER) cc_final: 0.6670 (mp) outliers start: 8 outliers final: 6 residues processed: 47 average time/residue: 0.0926 time to fit residues: 6.1572 Evaluate side-chains 49 residues out of total 327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 42 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 VAL Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 109 VAL Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 353 SER Chi-restraints excluded: chain A residue 421 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/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-5592/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/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-5592/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/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-5592/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-5592/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-5592/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-5592/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-5592/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-5592/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-5592/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-5592/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/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-5592/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-5592/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-5592/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-5592/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: 67.6539 > 50: distance: 1 - 20: 10.640 distance: 6 - 27: 21.865 distance: 10 - 35: 29.249 distance: 14 - 20: 11.356 distance: 20 - 21: 8.326 distance: 21 - 22: 14.935 distance: 21 - 24: 5.884 distance: 22 - 27: 15.785 distance: 23 - 50: 31.130 distance: 24 - 25: 16.187 distance: 24 - 26: 15.256 distance: 27 - 28: 30.902 distance: 28 - 29: 32.274 distance: 28 - 31: 32.612 distance: 29 - 30: 25.764 distance: 29 - 35: 20.221 distance: 30 - 62: 21.129 distance: 31 - 32: 20.397 distance: 32 - 33: 38.503 distance: 32 - 34: 20.244 distance: 35 - 36: 36.458 distance: 36 - 37: 40.109 distance: 36 - 39: 16.807 distance: 37 - 38: 38.342 distance: 37 - 42: 16.630 distance: 39 - 40: 22.795 distance: 39 - 41: 41.259 distance: 42 - 43: 30.903 distance: 43 - 44: 33.921 distance: 43 - 46: 27.673 distance: 44 - 45: 18.565 distance: 44 - 50: 29.446 distance: 46 - 47: 3.667 distance: 47 - 48: 37.866 distance: 47 - 49: 17.629 distance: 50 - 51: 18.248 distance: 51 - 52: 30.963 distance: 51 - 54: 30.157 distance: 52 - 53: 3.720 distance: 52 - 62: 30.187 distance: 54 - 55: 14.907 distance: 55 - 56: 14.986 distance: 55 - 57: 16.364 distance: 56 - 58: 15.394 distance: 57 - 59: 20.511 distance: 58 - 60: 7.136 distance: 59 - 60: 9.952 distance: 60 - 61: 9.033 distance: 62 - 63: 19.174 distance: 63 - 64: 56.854 distance: 63 - 66: 17.974 distance: 64 - 69: 37.838 distance: 66 - 67: 12.528 distance: 66 - 68: 13.466 distance: 69 - 70: 38.441 distance: 70 - 73: 39.891 distance: 71 - 72: 40.654 distance: 71 - 80: 9.409 distance: 73 - 74: 28.753 distance: 74 - 75: 23.355 distance: 75 - 76: 38.036 distance: 76 - 77: 17.800 distance: 77 - 78: 21.584 distance: 77 - 79: 23.988 distance: 80 - 81: 50.440 distance: 81 - 82: 48.113 distance: 81 - 84: 56.513 distance: 82 - 83: 43.283 distance: 82 - 92: 32.350 distance: 84 - 85: 9.491 distance: 85 - 86: 39.891 distance: 85 - 87: 23.369 distance: 86 - 88: 9.566 distance: 87 - 89: 10.751 distance: 88 - 90: 9.496 distance: 89 - 90: 8.767 distance: 92 - 93: 42.349 distance: 93 - 94: 57.186 distance: 93 - 96: 67.654 distance: 94 - 95: 34.897 distance: 94 - 101: 23.661 distance: 95 - 123: 27.744 distance: 96 - 97: 38.045 distance: 97 - 98: 15.555 distance: 98 - 99: 31.724 distance: 99 - 100: 29.231 distance: 101 - 102: 37.338 distance: 101 - 107: 38.291 distance: 102 - 103: 34.826 distance: 102 - 105: 24.897 distance: 103 - 104: 16.218 distance: 103 - 108: 13.619 distance: 104 - 131: 8.012 distance: 105 - 106: 22.195 distance: 106 - 107: 31.546