Starting phenix.real_space_refine on Fri Nov 15 14:41:22 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tq2_41499/11_2024/8tq2_41499_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tq2_41499/11_2024/8tq2_41499.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tq2_41499/11_2024/8tq2_41499.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tq2_41499/11_2024/8tq2_41499.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tq2_41499/11_2024/8tq2_41499_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tq2_41499/11_2024/8tq2_41499_neut.cif" } resolution = 3.8 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= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 4357 atoms to isotropic. 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 36 5.16 5 C 3569 2.51 5 N 931 2.21 5 O 969 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 5505 Number of models: 1 Model: "" Number of chains: 4 Chain: "C" Number of atoms: 639 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 639 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 8, 'TRANS': 73} Chain: "D" Number of atoms: 120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 120 Classifications: {'peptide': 16} Link IDs: {'PTRANS': 1, 'TRANS': 14} Chain: "A" Number of atoms: 2561 Number of conformers: 1 Conformer: "" Number of residues, atoms: 313, 2561 Classifications: {'peptide': 313} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 294} Chain breaks: 5 Chain: "B" Number of atoms: 2185 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 261, 2178 Classifications: {'peptide': 261} Link IDs: {'PTRANS': 12, 'TRANS': 248} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 261, 2178 Classifications: {'peptide': 261} Link IDs: {'PTRANS': 12, 'TRANS': 248} Chain breaks: 1 bond proxies already assigned to first conformer: 2226 Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N AVAL B 163 " occ=0.50 ... (12 atoms not shown) pdb=" CG2BVAL B 163 " occ=0.50 Time building chain proxies: 5.09, per 1000 atoms: 0.92 Number of scatterers: 5505 At special positions: 0 Unit cell: (81.3276, 101.659, 82.3977, 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 36 16.00 O 969 8.00 N 931 7.00 C 3569 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: 1.31 Conformation dependent library (CDL) restraints added in 1.1 seconds 1310 Ramachandran restraints generated. 655 Oldfield, 0 Emsley, 655 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1292 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 3 sheets defined 52.5% alpha, 5.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.53 Creating SS restraints... Processing helix chain 'C' and resid 37 through 44 removed outlier: 3.546A pdb=" N LYS C 42 " --> pdb=" O ALA C 38 " (cutoff:3.500A) Processing helix chain 'C' and resid 65 through 84 Processing helix chain 'D' and resid 1619 through 1623 removed outlier: 3.693A pdb=" N VAL D1622 " --> pdb=" O ARG D1619 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N GLY D1623 " --> pdb=" O ASP D1620 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 1619 through 1623' Processing helix chain 'A' and resid 2 through 13 Processing helix chain 'A' and resid 60 through 71 Processing helix chain 'A' and resid 104 through 111 Processing helix chain 'A' and resid 124 through 145 removed outlier: 3.629A pdb=" N VAL A 128 " --> pdb=" O PRO A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 153 through 155 No H-bonds generated for 'chain 'A' and resid 153 through 155' Processing helix chain 'A' and resid 201 through 206 Processing helix chain 'A' and resid 214 through 230 Processing helix chain 'A' and resid 251 through 260 removed outlier: 3.750A pdb=" N MET A 259 " --> pdb=" O ILE A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 292 through 300 removed outlier: 3.714A pdb=" N HIS A 300 " --> pdb=" O TYR A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 316 removed outlier: 3.949A pdb=" N HIS A 310 " --> pdb=" O SER A 306 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEU A 311 " --> pdb=" O LYS A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 325 through 332 removed outlier: 3.600A pdb=" N ALA A 329 " --> pdb=" O THR A 325 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N MET A 330 " --> pdb=" O SER A 326 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N GLN A 331 " --> pdb=" O GLU A 327 " (cutoff:3.500A) Processing helix chain 'B' and resid 8 through 13 Processing helix chain 'B' and resid 17 through 25 Processing helix chain 'B' and resid 25 through 30 Processing helix chain 'B' and resid 33 through 55 Processing helix chain 'B' and resid 58 through 70 removed outlier: 3.914A pdb=" N ILE B 62 " --> pdb=" O ARG B 58 " (cutoff:3.500A) Processing helix chain 'B' and resid 72 through 75 Processing helix chain 'B' and resid 82 through 98 Proline residue: B 88 - end of helix Processing helix chain 'B' and resid 104 through 120 removed outlier: 3.512A pdb=" N PHE B 120 " --> pdb=" O LEU B 116 " (cutoff:3.500A) Processing helix chain 'B' and resid 131 through 146 Processing helix chain 'B' and resid 155 through 167 Processing helix chain 'B' and resid 172 through 183 Processing helix chain 'B' and resid 184 through 186 No H-bonds generated for 'chain 'B' and resid 184 through 186' Processing helix chain 'B' and resid 187 through 192 Processing helix chain 'B' and resid 193 through 209 removed outlier: 3.535A pdb=" N ILE B 197 " --> pdb=" O PRO B 193 " (cutoff:3.500A) Processing helix chain 'B' and resid 213 through 220 removed outlier: 3.793A pdb=" N GLU B 219 " --> pdb=" O GLN B 215 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N LEU B 220 " --> pdb=" O TRP B 216 " (cutoff:3.500A) Processing helix chain 'B' and resid 225 through 241 Processing helix chain 'B' and resid 242 through 244 No H-bonds generated for 'chain 'B' and resid 242 through 244' Processing helix chain 'B' and resid 245 through 256 removed outlier: 3.619A pdb=" N GLU B 249 " --> pdb=" O ASP B 245 " (cutoff:3.500A) removed outlier: 4.794A pdb=" N ALA B 251 " --> pdb=" O ARG B 247 " (cutoff:3.500A) removed outlier: 5.251A pdb=" N THR B 252 " --> pdb=" O LYS B 248 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 26 through 29 removed outlier: 6.584A pdb=" N LYS A 26 " --> pdb=" O LYS A 37 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N LYS A 37 " --> pdb=" O LYS A 26 " (cutoff:3.500A) removed outlier: 5.143A pdb=" N VAL A 93 " --> pdb=" O ILE A 54 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N LYS A 92 " --> pdb=" O LEU A 86 " (cutoff:3.500A) removed outlier: 5.078A pdb=" N LEU A 86 " --> pdb=" O LYS A 92 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N TRP A 94 " --> pdb=" O VAL A 84 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N VAL A 84 " --> pdb=" O TRP A 94 " (cutoff:3.500A) removed outlier: 7.171A pdb=" N LEU A 96 " --> pdb=" O GLN A 82 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 102 through 103 removed outlier: 4.430A pdb=" N MET A 160 " --> pdb=" O ARG A 168 " (cutoff:3.500A) removed outlier: 5.530A pdb=" N ARG A 168 " --> pdb=" O MET A 160 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 147 through 148 230 hydrogen bonds defined for protein. 679 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: 1.30 Time building geometry restraints manager: 1.52 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 1743 1.35 - 1.46: 1291 1.46 - 1.58: 2552 1.58 - 1.70: 0 1.70 - 1.82: 58 Bond restraints: 5644 Sorted by residual: bond pdb=" C MET A 273 " pdb=" N PRO A 274 " ideal model delta sigma weight residual 1.334 1.356 -0.022 2.34e-02 1.83e+03 9.03e-01 bond pdb=" CB GLU B 98 " pdb=" CG GLU B 98 " ideal model delta sigma weight residual 1.520 1.545 -0.025 3.00e-02 1.11e+03 6.99e-01 bond pdb=" CG GLU B 98 " pdb=" CD GLU B 98 " ideal model delta sigma weight residual 1.516 1.536 -0.020 2.50e-02 1.60e+03 6.59e-01 bond pdb=" CA ASP A 137 " pdb=" CB ASP A 137 " ideal model delta sigma weight residual 1.528 1.541 -0.013 1.59e-02 3.96e+03 6.43e-01 bond pdb=" N PRO B 193 " pdb=" CA PRO B 193 " ideal model delta sigma weight residual 1.457 1.467 -0.010 1.31e-02 5.83e+03 6.20e-01 ... (remaining 5639 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.53: 7458 1.53 - 3.05: 125 3.05 - 4.58: 32 4.58 - 6.10: 7 6.10 - 7.63: 3 Bond angle restraints: 7625 Sorted by residual: angle pdb=" CB MET B 250 " pdb=" CG MET B 250 " pdb=" SD MET B 250 " ideal model delta sigma weight residual 112.70 120.33 -7.63 3.00e+00 1.11e-01 6.47e+00 angle pdb=" CB MET B 86 " pdb=" CG MET B 86 " pdb=" SD MET B 86 " ideal model delta sigma weight residual 112.70 120.32 -7.62 3.00e+00 1.11e-01 6.46e+00 angle pdb=" CA MET A 174 " pdb=" CB MET A 174 " pdb=" CG MET A 174 " ideal model delta sigma weight residual 114.10 118.42 -4.32 2.00e+00 2.50e-01 4.67e+00 angle pdb=" C LEU A 69 " pdb=" N LEU A 70 " pdb=" CA LEU A 70 " ideal model delta sigma weight residual 121.94 117.69 4.25 2.00e+00 2.50e-01 4.52e+00 angle pdb=" C LYS C 15 " pdb=" N ARG C 16 " pdb=" CA ARG C 16 " ideal model delta sigma weight residual 120.58 123.32 -2.74 1.32e+00 5.74e-01 4.29e+00 ... (remaining 7620 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.18: 2991 16.18 - 32.35: 337 32.35 - 48.53: 71 48.53 - 64.70: 10 64.70 - 80.88: 7 Dihedral angle restraints: 3416 sinusoidal: 1431 harmonic: 1985 Sorted by residual: dihedral pdb=" CA ASP B 20 " pdb=" CB ASP B 20 " pdb=" CG ASP B 20 " pdb=" OD1 ASP B 20 " ideal model delta sinusoidal sigma weight residual -30.00 -81.65 51.65 1 2.00e+01 2.50e-03 9.11e+00 dihedral pdb=" CG ARG B 58 " pdb=" CD ARG B 58 " pdb=" NE ARG B 58 " pdb=" CZ ARG B 58 " ideal model delta sinusoidal sigma weight residual 180.00 139.55 40.45 2 1.50e+01 4.44e-03 8.98e+00 dihedral pdb=" CB GLU A 101 " pdb=" CG GLU A 101 " pdb=" CD GLU A 101 " pdb=" OE1 GLU A 101 " ideal model delta sinusoidal sigma weight residual 0.00 80.88 -80.88 1 3.00e+01 1.11e-03 8.98e+00 ... (remaining 3413 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 481 0.028 - 0.057: 204 0.057 - 0.085: 90 0.085 - 0.113: 47 0.113 - 0.141: 5 Chirality restraints: 827 Sorted by residual: chirality pdb=" CA VAL B 222 " pdb=" N VAL B 222 " pdb=" C VAL B 222 " pdb=" CB VAL B 222 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 5.00e-01 chirality pdb=" CA LEU A 70 " pdb=" N LEU A 70 " pdb=" C LEU A 70 " pdb=" CB LEU A 70 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.16e-01 chirality pdb=" CA VAL A 195 " pdb=" N VAL A 195 " pdb=" C VAL A 195 " pdb=" CB VAL A 195 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.69e-01 ... (remaining 824 not shown) Planarity restraints: 964 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR C 25 " 0.027 5.00e-02 4.00e+02 4.11e-02 2.70e+00 pdb=" N PRO C 26 " -0.071 5.00e-02 4.00e+02 pdb=" CA PRO C 26 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO C 26 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 340 " 0.021 5.00e-02 4.00e+02 3.19e-02 1.63e+00 pdb=" N PRO A 341 " -0.055 5.00e-02 4.00e+02 pdb=" CA PRO A 341 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO A 341 " 0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP C 28 " 0.019 5.00e-02 4.00e+02 2.86e-02 1.31e+00 pdb=" N PRO C 29 " -0.050 5.00e-02 4.00e+02 pdb=" CA PRO C 29 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO C 29 " 0.016 5.00e-02 4.00e+02 ... (remaining 961 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 1376 2.80 - 3.33: 5197 3.33 - 3.85: 8567 3.85 - 4.38: 9625 4.38 - 4.90: 16927 Nonbonded interactions: 41692 Sorted by model distance: nonbonded pdb=" OE2 GLU A 203 " pdb=" NH2 ARG A 323 " model vdw 2.278 3.120 nonbonded pdb=" O LYS B 70 " pdb=" N PHE B 72 " model vdw 2.283 3.120 nonbonded pdb=" O THR B 252 " pdb=" OG SER B 255 " model vdw 2.284 3.040 nonbonded pdb=" O ILE A 59 " pdb=" NZ LYS B 96 " model vdw 2.300 3.120 nonbonded pdb=" NE2 GLN C 27 " pdb=" O HIS A 143 " model vdw 2.332 3.120 ... (remaining 41687 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=0.98 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 3.090 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.060 Construct map_model_manager: 0.010 Extract box with map and model: 0.210 Check model and map are aligned: 0.040 Set scattering table: 0.070 Process input model: 17.750 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.030 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:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7840 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 : 0.002 0.031 5644 Z= 0.145 Angle : 0.551 7.630 7625 Z= 0.276 Chirality : 0.041 0.141 827 Planarity : 0.004 0.041 964 Dihedral : 14.159 80.877 2124 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 0.00 % Allowed : 0.50 % Favored : 99.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.72 (0.33), residues: 655 helix: 1.66 (0.31), residues: 311 sheet: 1.88 (1.30), residues: 13 loop : -0.75 (0.32), residues: 331 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 38 HIS 0.001 0.000 HIS A 34 PHE 0.011 0.001 PHE B 140 TYR 0.007 0.001 TYR C 25 ARG 0.008 0.000 ARG A 209 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1310 Ramachandran restraints generated. 655 Oldfield, 0 Emsley, 655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1310 Ramachandran restraints generated. 655 Oldfield, 0 Emsley, 655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 96 time to evaluate : 0.644 Fit side-chains REVERT: D 1617 MET cc_start: 0.5644 (mmp) cc_final: 0.4255 (tmm) REVERT: A 61 MET cc_start: 0.7989 (mmm) cc_final: 0.7777 (mmm) outliers start: 0 outliers final: 0 residues processed: 96 average time/residue: 0.1650 time to fit residues: 21.2530 Evaluate side-chains 67 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 67 time to evaluate : 0.635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 55 optimal weight: 2.9990 chunk 50 optimal weight: 0.8980 chunk 27 optimal weight: 3.9990 chunk 17 optimal weight: 1.9990 chunk 33 optimal weight: 6.9990 chunk 26 optimal weight: 6.9990 chunk 51 optimal weight: 1.9990 chunk 20 optimal weight: 0.9990 chunk 31 optimal weight: 2.9990 chunk 38 optimal weight: 4.9990 chunk 59 optimal weight: 0.4980 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D1631 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.1336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 5644 Z= 0.262 Angle : 0.592 10.857 7625 Z= 0.296 Chirality : 0.044 0.150 827 Planarity : 0.004 0.033 964 Dihedral : 3.827 17.339 728 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 0.83 % Allowed : 7.97 % Favored : 91.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.66 (0.32), residues: 655 helix: 1.42 (0.30), residues: 317 sheet: -0.41 (0.94), residues: 25 loop : -0.48 (0.34), residues: 313 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 38 HIS 0.005 0.001 HIS A 310 PHE 0.010 0.001 PHE A 180 TYR 0.014 0.001 TYR B 184 ARG 0.003 0.000 ARG A 178 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1310 Ramachandran restraints generated. 655 Oldfield, 0 Emsley, 655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1310 Ramachandran restraints generated. 655 Oldfield, 0 Emsley, 655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 68 time to evaluate : 0.688 Fit side-chains REVERT: D 1617 MET cc_start: 0.5797 (mmp) cc_final: 0.4344 (tmm) outliers start: 5 outliers final: 3 residues processed: 71 average time/residue: 0.1358 time to fit residues: 13.9390 Evaluate side-chains 67 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 64 time to evaluate : 0.652 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 71 SER Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain B residue 47 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 33 optimal weight: 6.9990 chunk 18 optimal weight: 6.9990 chunk 49 optimal weight: 1.9990 chunk 40 optimal weight: 0.2980 chunk 16 optimal weight: 2.9990 chunk 60 optimal weight: 2.9990 chunk 64 optimal weight: 3.9990 chunk 53 optimal weight: 0.6980 chunk 59 optimal weight: 0.7980 chunk 20 optimal weight: 2.9990 chunk 48 optimal weight: 0.0980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 40 ASN D1631 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7936 moved from start: 0.1492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 5644 Z= 0.180 Angle : 0.537 8.823 7625 Z= 0.265 Chirality : 0.042 0.139 827 Planarity : 0.004 0.032 964 Dihedral : 3.757 15.591 728 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 1.16 % Allowed : 10.30 % Favored : 88.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.77 (0.33), residues: 655 helix: 1.46 (0.30), residues: 319 sheet: -0.18 (0.95), residues: 25 loop : -0.39 (0.34), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 38 HIS 0.005 0.001 HIS D1631 PHE 0.010 0.001 PHE B 44 TYR 0.008 0.001 TYR B 184 ARG 0.006 0.000 ARG C 16 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1310 Ramachandran restraints generated. 655 Oldfield, 0 Emsley, 655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1310 Ramachandran restraints generated. 655 Oldfield, 0 Emsley, 655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 69 time to evaluate : 0.521 Fit side-chains REVERT: D 1617 MET cc_start: 0.5931 (mmp) cc_final: 0.4442 (tmm) REVERT: A 107 ILE cc_start: 0.9335 (OUTLIER) cc_final: 0.9053 (mm) REVERT: B 138 CYS cc_start: 0.8815 (t) cc_final: 0.8611 (t) outliers start: 7 outliers final: 3 residues processed: 75 average time/residue: 0.1293 time to fit residues: 14.1318 Evaluate side-chains 71 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 67 time to evaluate : 0.635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 ILE Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain A residue 324 ILE Chi-restraints excluded: chain B residue 47 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 59 optimal weight: 0.5980 chunk 45 optimal weight: 3.9990 chunk 31 optimal weight: 2.9990 chunk 6 optimal weight: 0.0980 chunk 28 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 chunk 60 optimal weight: 0.9980 chunk 63 optimal weight: 0.8980 chunk 57 optimal weight: 0.5980 chunk 17 optimal weight: 0.6980 chunk 53 optimal weight: 0.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D1631 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7929 moved from start: 0.1648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 5644 Z= 0.159 Angle : 0.501 5.953 7625 Z= 0.253 Chirality : 0.042 0.151 827 Planarity : 0.004 0.044 964 Dihedral : 3.704 14.693 728 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 1.16 % Allowed : 11.46 % Favored : 87.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.77 (0.33), residues: 655 helix: 1.42 (0.30), residues: 320 sheet: -0.08 (0.96), residues: 25 loop : -0.35 (0.35), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 38 HIS 0.004 0.001 HIS D1631 PHE 0.010 0.001 PHE B 44 TYR 0.007 0.001 TYR B 76 ARG 0.001 0.000 ARG A 323 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1310 Ramachandran restraints generated. 655 Oldfield, 0 Emsley, 655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1310 Ramachandran restraints generated. 655 Oldfield, 0 Emsley, 655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 69 time to evaluate : 0.701 Fit side-chains REVERT: D 1617 MET cc_start: 0.5953 (mmp) cc_final: 0.4423 (ppp) REVERT: A 107 ILE cc_start: 0.9334 (OUTLIER) cc_final: 0.9042 (mm) REVERT: B 132 MET cc_start: 0.7493 (tpt) cc_final: 0.7236 (tpp) outliers start: 7 outliers final: 3 residues processed: 75 average time/residue: 0.1330 time to fit residues: 14.3780 Evaluate side-chains 69 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 65 time to evaluate : 0.645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 ILE Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain A residue 324 ILE Chi-restraints excluded: chain B residue 47 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 36 optimal weight: 0.6980 chunk 0 optimal weight: 3.9990 chunk 47 optimal weight: 2.9990 chunk 26 optimal weight: 0.7980 chunk 54 optimal weight: 0.9980 chunk 44 optimal weight: 2.9990 chunk 32 optimal weight: 4.9990 chunk 57 optimal weight: 0.0870 chunk 16 optimal weight: 0.7980 chunk 21 optimal weight: 3.9990 chunk 12 optimal weight: 8.9990 overall best weight: 0.6758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.1737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 5644 Z= 0.169 Angle : 0.513 6.459 7625 Z= 0.255 Chirality : 0.042 0.165 827 Planarity : 0.004 0.043 964 Dihedral : 3.703 14.485 728 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 1.33 % Allowed : 12.62 % Favored : 86.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.80 (0.33), residues: 655 helix: 1.41 (0.29), residues: 320 sheet: 0.01 (0.96), residues: 25 loop : -0.29 (0.35), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 38 HIS 0.003 0.001 HIS A 88 PHE 0.010 0.001 PHE B 44 TYR 0.008 0.001 TYR B 76 ARG 0.007 0.000 ARG C 16 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1310 Ramachandran restraints generated. 655 Oldfield, 0 Emsley, 655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1310 Ramachandran restraints generated. 655 Oldfield, 0 Emsley, 655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 65 time to evaluate : 0.621 Fit side-chains REVERT: D 1617 MET cc_start: 0.5938 (mmp) cc_final: 0.4401 (ppp) REVERT: A 107 ILE cc_start: 0.9340 (OUTLIER) cc_final: 0.9050 (mm) outliers start: 8 outliers final: 5 residues processed: 73 average time/residue: 0.1282 time to fit residues: 13.7724 Evaluate side-chains 69 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 63 time to evaluate : 0.714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 107 ILE Chi-restraints excluded: chain A residue 137 ASP Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain A residue 324 ILE Chi-restraints excluded: chain B residue 47 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 37 optimal weight: 0.6980 chunk 15 optimal weight: 2.9990 chunk 63 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 5 optimal weight: 9.9990 chunk 21 optimal weight: 0.9990 chunk 33 optimal weight: 5.9990 chunk 61 optimal weight: 3.9990 chunk 7 optimal weight: 1.9990 chunk 36 optimal weight: 6.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 moved from start: 0.2103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 5644 Z= 0.294 Angle : 0.595 8.196 7625 Z= 0.293 Chirality : 0.044 0.167 827 Planarity : 0.004 0.043 964 Dihedral : 4.010 14.983 728 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 1.50 % Allowed : 13.62 % Favored : 84.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.51 (0.33), residues: 655 helix: 1.14 (0.29), residues: 321 sheet: 0.02 (0.98), residues: 25 loop : -0.43 (0.35), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 38 HIS 0.003 0.001 HIS C 56 PHE 0.010 0.001 PHE C 73 TYR 0.013 0.001 TYR B 184 ARG 0.003 0.000 ARG A 178 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1310 Ramachandran restraints generated. 655 Oldfield, 0 Emsley, 655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1310 Ramachandran restraints generated. 655 Oldfield, 0 Emsley, 655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 67 time to evaluate : 0.687 Fit side-chains REVERT: D 1617 MET cc_start: 0.6107 (mmp) cc_final: 0.4439 (ppp) REVERT: A 107 ILE cc_start: 0.9355 (OUTLIER) cc_final: 0.9072 (mm) REVERT: B 38 TRP cc_start: 0.8173 (t60) cc_final: 0.7759 (t60) REVERT: B 132 MET cc_start: 0.7629 (tpt) cc_final: 0.7304 (tpp) REVERT: B 250 MET cc_start: 0.7949 (mmm) cc_final: 0.7667 (mmm) outliers start: 8 outliers final: 4 residues processed: 74 average time/residue: 0.1548 time to fit residues: 16.1812 Evaluate side-chains 67 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 62 time to evaluate : 0.733 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 107 ILE Chi-restraints excluded: chain A residue 196 THR Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain B residue 47 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 46 optimal weight: 0.8980 chunk 36 optimal weight: 1.9990 chunk 53 optimal weight: 0.6980 chunk 35 optimal weight: 0.9990 chunk 63 optimal weight: 1.9990 chunk 39 optimal weight: 0.7980 chunk 38 optimal weight: 1.9990 chunk 29 optimal weight: 0.9980 chunk 25 optimal weight: 0.9980 chunk 37 optimal weight: 0.7980 chunk 19 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7967 moved from start: 0.2118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 5644 Z= 0.191 Angle : 0.555 9.203 7625 Z= 0.275 Chirality : 0.042 0.151 827 Planarity : 0.004 0.043 964 Dihedral : 3.907 15.578 728 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 2.33 % Allowed : 14.45 % Favored : 83.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.65 (0.33), residues: 655 helix: 1.25 (0.29), residues: 320 sheet: 0.08 (1.01), residues: 25 loop : -0.34 (0.36), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 38 HIS 0.003 0.001 HIS A 88 PHE 0.029 0.001 PHE A 261 TYR 0.008 0.001 TYR B 76 ARG 0.001 0.000 ARG D1619 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1310 Ramachandran restraints generated. 655 Oldfield, 0 Emsley, 655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1310 Ramachandran restraints generated. 655 Oldfield, 0 Emsley, 655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 63 time to evaluate : 0.672 Fit side-chains REVERT: D 1617 MET cc_start: 0.6119 (mmp) cc_final: 0.4522 (ppp) REVERT: A 107 ILE cc_start: 0.9350 (OUTLIER) cc_final: 0.9074 (mm) REVERT: B 132 MET cc_start: 0.7558 (tpt) cc_final: 0.7242 (tpp) REVERT: B 250 MET cc_start: 0.7808 (mmm) cc_final: 0.7559 (mmm) outliers start: 13 outliers final: 10 residues processed: 73 average time/residue: 0.1293 time to fit residues: 13.8378 Evaluate side-chains 74 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 63 time to evaluate : 0.657 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 40 ASN Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 107 ILE Chi-restraints excluded: chain A residue 137 ASP Chi-restraints excluded: chain A residue 196 THR Chi-restraints excluded: chain A residue 203 GLU Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain A residue 324 ILE Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 171 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 12 optimal weight: 9.9990 chunk 40 optimal weight: 3.9990 chunk 43 optimal weight: 0.9990 chunk 31 optimal weight: 3.9990 chunk 5 optimal weight: 9.9990 chunk 50 optimal weight: 2.9990 chunk 57 optimal weight: 0.8980 chunk 60 optimal weight: 1.9990 chunk 55 optimal weight: 0.9980 chunk 59 optimal weight: 0.6980 chunk 35 optimal weight: 2.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.2263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 5644 Z= 0.230 Angle : 0.573 8.282 7625 Z= 0.284 Chirality : 0.043 0.141 827 Planarity : 0.004 0.042 964 Dihedral : 3.984 18.888 728 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 2.33 % Allowed : 14.95 % Favored : 82.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.33), residues: 655 helix: 1.21 (0.29), residues: 320 sheet: 0.05 (1.03), residues: 25 loop : -0.35 (0.36), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 38 HIS 0.003 0.001 HIS A 88 PHE 0.025 0.001 PHE A 261 TYR 0.010 0.001 TYR B 184 ARG 0.002 0.000 ARG A 65 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1310 Ramachandran restraints generated. 655 Oldfield, 0 Emsley, 655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1310 Ramachandran restraints generated. 655 Oldfield, 0 Emsley, 655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 61 time to evaluate : 0.735 Fit side-chains REVERT: C 40 ASN cc_start: 0.7246 (OUTLIER) cc_final: 0.7018 (m-40) REVERT: D 1617 MET cc_start: 0.6151 (mmp) cc_final: 0.4498 (ppp) REVERT: A 107 ILE cc_start: 0.9346 (OUTLIER) cc_final: 0.9073 (mm) REVERT: B 132 MET cc_start: 0.7604 (tpt) cc_final: 0.7270 (tpp) REVERT: B 246 GLU cc_start: 0.7071 (mm-30) cc_final: 0.6740 (mm-30) REVERT: B 250 MET cc_start: 0.7887 (mmm) cc_final: 0.7587 (mmm) outliers start: 13 outliers final: 8 residues processed: 71 average time/residue: 0.1407 time to fit residues: 14.4031 Evaluate side-chains 71 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 61 time to evaluate : 0.650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 40 ASN Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 107 ILE Chi-restraints excluded: chain A residue 137 ASP Chi-restraints excluded: chain A residue 196 THR Chi-restraints excluded: chain A residue 203 GLU Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 171 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/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-5513/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/phenix/phenix/programs/real_space_refine.py", line 213, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/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-5513/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/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-5513/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 766, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/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-5513/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-5513/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-5513/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-5513/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-5513/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-5513/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/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-5513/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-5513/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-5513/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-5513/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: 58.6355 > 50: distance: 97 - 102: 32.384 distance: 102 - 103: 17.263 distance: 103 - 104: 22.788 distance: 103 - 106: 18.074 distance: 104 - 105: 22.189 distance: 104 - 110: 20.339 distance: 106 - 107: 19.108 distance: 107 - 108: 20.894 distance: 107 - 109: 30.033 distance: 110 - 111: 20.209 distance: 111 - 112: 13.917 distance: 111 - 114: 29.969 distance: 112 - 113: 8.482 distance: 112 - 119: 34.495 distance: 114 - 115: 24.492 distance: 115 - 116: 27.394 distance: 116 - 117: 9.814 distance: 116 - 118: 17.136 distance: 119 - 120: 37.910 distance: 120 - 121: 27.921 distance: 120 - 123: 14.091 distance: 121 - 122: 19.873 distance: 121 - 127: 11.757 distance: 123 - 124: 35.571 distance: 124 - 125: 13.394 distance: 124 - 126: 28.402 distance: 127 - 128: 28.273 distance: 127 - 133: 21.239 distance: 128 - 129: 18.470 distance: 128 - 131: 43.032 distance: 129 - 130: 9.659 distance: 129 - 134: 14.578 distance: 131 - 132: 28.532 distance: 132 - 133: 37.941 distance: 134 - 135: 38.679 distance: 135 - 136: 41.091 distance: 135 - 138: 23.106 distance: 136 - 137: 21.574 distance: 136 - 142: 38.860 distance: 138 - 139: 33.168 distance: 139 - 141: 7.922 distance: 142 - 143: 37.268 distance: 142 - 148: 26.413 distance: 143 - 144: 21.471 distance: 143 - 146: 19.540 distance: 144 - 145: 21.515 distance: 144 - 149: 11.404 distance: 146 - 147: 16.582 distance: 147 - 148: 20.856 distance: 149 - 150: 6.964 distance: 150 - 151: 10.955 distance: 150 - 153: 27.340 distance: 151 - 152: 7.893 distance: 151 - 156: 8.445 distance: 153 - 154: 24.007 distance: 153 - 155: 7.709 distance: 156 - 157: 26.299 distance: 157 - 158: 9.467 distance: 157 - 160: 29.463 distance: 158 - 159: 26.353 distance: 158 - 162: 21.040 distance: 160 - 161: 25.930 distance: 162 - 163: 23.753 distance: 163 - 164: 20.273 distance: 163 - 166: 13.605 distance: 164 - 165: 15.516 distance: 164 - 170: 5.728 distance: 166 - 167: 32.654 distance: 167 - 168: 22.054 distance: 167 - 169: 35.264 distance: 170 - 171: 11.845 distance: 171 - 172: 41.334 distance: 171 - 174: 29.497 distance: 172 - 173: 9.165 distance: 172 - 177: 28.129 distance: 174 - 175: 39.835 distance: 174 - 176: 6.876