Starting phenix.real_space_refine on Tue Jan 14 15:32:12 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9b3k_44143/01_2025/9b3k_44143.cif Found real_map, /net/cci-nas-00/data/ceres_data/9b3k_44143/01_2025/9b3k_44143.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.56 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9b3k_44143/01_2025/9b3k_44143.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9b3k_44143/01_2025/9b3k_44143.map" model { file = "/net/cci-nas-00/data/ceres_data/9b3k_44143/01_2025/9b3k_44143.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9b3k_44143/01_2025/9b3k_44143.cif" } resolution = 2.56 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= 0.038 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 960 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 27 5.16 5 C 3940 2.51 5 N 972 2.21 5 O 1124 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 6063 Number of models: 1 Model: "" Number of chains: 3 Chain: "Z" Number of atoms: 2833 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 2833 Classifications: {'peptide': 370} Link IDs: {'PTRANS': 13, 'TRANS': 356} Chain breaks: 1 Chain: "H" Number of atoms: 1687 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1687 Classifications: {'peptide': 224} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 212} Chain breaks: 1 Chain: "L" Number of atoms: 1543 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 203, 1540 Classifications: {'peptide': 203} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 192} Chain breaks: 4 Conformer: "B" Number of residues, atoms: 203, 1540 Classifications: {'peptide': 203} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 192} Chain breaks: 4 bond proxies already assigned to first conformer: 1563 Time building chain proxies: 5.49, per 1000 atoms: 0.91 Number of scatterers: 6063 At special positions: 0 Unit cell: (66.825, 65.175, 129.525, 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 27 16.00 O 1124 8.00 N 972 7.00 C 3940 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS H 48 " - pdb=" SG CYS H 122 " distance=2.03 Simple disulfide: pdb=" SG CYS H 181 " - pdb=" SG CYS H 237 " distance=2.03 Simple disulfide: pdb=" SG CYS L 47 " - pdb=" SG CYS L 112 " distance=2.03 Simple disulfide: pdb=" SG CYS L 158 " - pdb=" SG CYS L 218 " distance=2.03 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: 1.58 Conformation dependent library (CDL) restraints added in 1.1 seconds 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1452 Finding SS restraints... Secondary structure from input PDB file: 22 helices and 12 sheets defined 46.0% alpha, 31.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.72 Creating SS restraints... Processing helix chain 'Z' and resid 3 through 21 removed outlier: 3.561A pdb=" N GLY Z 20 " --> pdb=" O PHE Z 16 " (cutoff:3.500A) Processing helix chain 'Z' and resid 22 through 24 No H-bonds generated for 'chain 'Z' and resid 22 through 24' Processing helix chain 'Z' and resid 25 through 34 Processing helix chain 'Z' and resid 36 through 66 removed outlier: 4.217A pdb=" N PHE Z 47 " --> pdb=" O LEU Z 43 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N ALA Z 48 " --> pdb=" O VAL Z 44 " (cutoff:3.500A) Proline residue: Z 56 - end of helix Processing helix chain 'Z' and resid 66 through 88 removed outlier: 3.709A pdb=" N ILE Z 70 " --> pdb=" O GLY Z 66 " (cutoff:3.500A) Processing helix chain 'Z' and resid 90 through 119 Proline residue: Z 110 - end of helix Processing helix chain 'Z' and resid 124 through 150 Proline residue: Z 144 - end of helix Processing helix chain 'Z' and resid 156 through 177 Processing helix chain 'Z' and resid 204 through 224 removed outlier: 3.740A pdb=" N ALA Z 220 " --> pdb=" O PHE Z 216 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N PHE Z 221 " --> pdb=" O GLY Z 217 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LEU Z 224 " --> pdb=" O ALA Z 220 " (cutoff:3.500A) Processing helix chain 'Z' and resid 224 through 234 removed outlier: 3.559A pdb=" N ASN Z 234 " --> pdb=" O ALA Z 230 " (cutoff:3.500A) Processing helix chain 'Z' and resid 236 through 258 Processing helix chain 'Z' and resid 258 through 266 Processing helix chain 'Z' and resid 267 through 288 Processing helix chain 'Z' and resid 291 through 302 removed outlier: 3.779A pdb=" N VAL Z 301 " --> pdb=" O LEU Z 297 " (cutoff:3.500A) Processing helix chain 'Z' and resid 303 through 321 removed outlier: 3.696A pdb=" N ARG Z 310 " --> pdb=" O PHE Z 306 " (cutoff:3.500A) Proline residue: Z 311 - end of helix Processing helix chain 'Z' and resid 324 through 352 Proline residue: Z 344 - end of helix removed outlier: 3.579A pdb=" N ALA Z 349 " --> pdb=" O LEU Z 345 " (cutoff:3.500A) Processing helix chain 'Z' and resid 356 through 384 Processing helix chain 'H' and resid 113 through 117 removed outlier: 3.672A pdb=" N THR H 117 " --> pdb=" O ALA H 114 " (cutoff:3.500A) Processing helix chain 'H' and resid 228 through 230 No H-bonds generated for 'chain 'H' and resid 228 through 230' Processing helix chain 'L' and resid 103 through 107 removed outlier: 3.999A pdb=" N PHE L 107 " --> pdb=" O PRO L 104 " (cutoff:3.500A) Processing helix chain 'L' and resid 145 through 152 removed outlier: 3.689A pdb=" N GLY L 152 " --> pdb=" O GLN L 148 " (cutoff:3.500A) Processing helix chain 'L' and resid 207 through 212 removed outlier: 3.629A pdb=" N LYS L 212 " --> pdb=" O ALA L 208 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'H' and resid 29 through 33 Processing sheet with id=AA2, first strand: chain 'H' and resid 84 through 86 removed outlier: 6.637A pdb=" N TRP H 62 " --> pdb=" O VAL H 74 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N SER H 76 " --> pdb=" O ILE H 60 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N ILE H 60 " --> pdb=" O SER H 76 " (cutoff:3.500A) removed outlier: 5.697A pdb=" N SER H 78 " --> pdb=" O SER H 58 " (cutoff:3.500A) removed outlier: 8.394A pdb=" N SER H 58 " --> pdb=" O SER H 78 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 84 through 86 removed outlier: 6.637A pdb=" N TRP H 62 " --> pdb=" O VAL H 74 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N SER H 76 " --> pdb=" O ILE H 60 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N ILE H 60 " --> pdb=" O SER H 76 " (cutoff:3.500A) removed outlier: 5.697A pdb=" N SER H 78 " --> pdb=" O SER H 58 " (cutoff:3.500A) removed outlier: 8.394A pdb=" N SER H 58 " --> pdb=" O SER H 78 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N CYS H 122 " --> pdb=" O TRP H 145 " (cutoff:3.500A) removed outlier: 4.725A pdb=" N TRP H 145 " --> pdb=" O CYS H 122 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N ARG H 124 " --> pdb=" O ASP H 143 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ALA H 132 " --> pdb=" O VAL H 135 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 161 through 165 removed outlier: 3.785A pdb=" N GLY H 180 " --> pdb=" O LEU H 165 " (cutoff:3.500A) removed outlier: 5.792A pdb=" N TYR H 217 " --> pdb=" O ASP H 185 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 161 through 165 removed outlier: 3.785A pdb=" N GLY H 180 " --> pdb=" O LEU H 165 " (cutoff:3.500A) removed outlier: 5.792A pdb=" N TYR H 217 " --> pdb=" O ASP H 185 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 191 through 195 removed outlier: 4.017A pdb=" N TYR H 235 " --> pdb=" O VAL H 252 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'L' and resid 30 through 31 Processing sheet with id=AA8, first strand: chain 'L' and resid 34 through 37 removed outlier: 6.430A pdb=" N TRP L 59 " --> pdb=" O LEU L 71 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'L' and resid 34 through 37 Processing sheet with id=AB1, first strand: chain 'L' and resid 140 through 142 removed outlier: 3.664A pdb=" N VAL L 157 " --> pdb=" O PHE L 142 " (cutoff:3.500A) removed outlier: 5.757A pdb=" N TYR L 197 " --> pdb=" O ASN L 162 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'L' and resid 169 through 169 Processing sheet with id=AB3, first strand: chain 'L' and resid 169 through 169 421 hydrogen bonds defined for protein. 1182 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: 2.11 Time building geometry restraints manager: 1.80 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1846 1.34 - 1.46: 1409 1.46 - 1.58: 2907 1.58 - 1.69: 0 1.69 - 1.81: 45 Bond restraints: 6207 Sorted by residual: bond pdb=" C VAL H 135 " pdb=" N GLY H 136 " ideal model delta sigma weight residual 1.328 1.310 0.018 1.31e-02 5.83e+03 1.89e+00 bond pdb=" N TRP H 133 " pdb=" CA TRP H 133 " ideal model delta sigma weight residual 1.457 1.471 -0.014 1.29e-02 6.01e+03 1.12e+00 bond pdb=" CB ASP H 143 " pdb=" CG ASP H 143 " ideal model delta sigma weight residual 1.516 1.490 0.026 2.50e-02 1.60e+03 1.04e+00 bond pdb=" CG PRO Z 311 " pdb=" CD PRO Z 311 " ideal model delta sigma weight residual 1.503 1.475 0.028 3.40e-02 8.65e+02 6.92e-01 bond pdb=" CB PRO Z 207 " pdb=" CG PRO Z 207 " ideal model delta sigma weight residual 1.492 1.452 0.040 5.00e-02 4.00e+02 6.28e-01 ... (remaining 6202 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.71: 8250 1.71 - 3.42: 141 3.42 - 5.13: 19 5.13 - 6.85: 10 6.85 - 8.56: 1 Bond angle restraints: 8421 Sorted by residual: angle pdb=" N VAL Z 153 " pdb=" CA VAL Z 153 " pdb=" C VAL Z 153 " ideal model delta sigma weight residual 112.96 108.86 4.10 1.00e+00 1.00e+00 1.68e+01 angle pdb=" N GLU H 189 " pdb=" CA GLU H 189 " pdb=" C GLU H 189 " ideal model delta sigma weight residual 109.81 116.19 -6.38 2.21e+00 2.05e-01 8.34e+00 angle pdb=" N VAL H 135 " pdb=" CA VAL H 135 " pdb=" C VAL H 135 " ideal model delta sigma weight residual 109.34 103.45 5.89 2.08e+00 2.31e-01 8.02e+00 angle pdb=" C TRP H 133 " pdb=" CA TRP H 133 " pdb=" CB TRP H 133 " ideal model delta sigma weight residual 110.42 116.05 -5.63 1.99e+00 2.53e-01 8.00e+00 angle pdb=" CA LEU L 199 " pdb=" CB LEU L 199 " pdb=" CG LEU L 199 " ideal model delta sigma weight residual 116.30 124.86 -8.56 3.50e+00 8.16e-02 5.98e+00 ... (remaining 8416 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.86: 3134 17.86 - 35.71: 362 35.71 - 53.57: 101 53.57 - 71.43: 26 71.43 - 89.28: 6 Dihedral angle restraints: 3629 sinusoidal: 1351 harmonic: 2278 Sorted by residual: dihedral pdb=" CB CYS H 181 " pdb=" SG CYS H 181 " pdb=" SG CYS H 237 " pdb=" CB CYS H 237 " ideal model delta sinusoidal sigma weight residual -86.00 -149.73 63.73 1 1.00e+01 1.00e-02 5.35e+01 dihedral pdb=" CA GLU H 189 " pdb=" C GLU H 189 " pdb=" N PRO H 190 " pdb=" CA PRO H 190 " ideal model delta harmonic sigma weight residual 180.00 152.86 27.14 0 5.00e+00 4.00e-02 2.95e+01 dihedral pdb=" CB CYS H 48 " pdb=" SG CYS H 48 " pdb=" SG CYS H 122 " pdb=" CB CYS H 122 " ideal model delta sinusoidal sigma weight residual 93.00 58.29 34.71 1 1.00e+01 1.00e-02 1.71e+01 ... (remaining 3626 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 719 0.043 - 0.086: 184 0.086 - 0.129: 57 0.129 - 0.172: 5 0.172 - 0.215: 2 Chirality restraints: 967 Sorted by residual: chirality pdb=" CB VAL Z 233 " pdb=" CA VAL Z 233 " pdb=" CG1 VAL Z 233 " pdb=" CG2 VAL Z 233 " both_signs ideal model delta sigma weight residual False -2.63 -2.41 -0.21 2.00e-01 2.50e+01 1.15e+00 chirality pdb=" CA THR Z 206 " pdb=" N THR Z 206 " pdb=" C THR Z 206 " pdb=" CB THR Z 206 " both_signs ideal model delta sigma weight residual False 2.53 2.34 0.19 2.00e-01 2.50e+01 8.80e-01 chirality pdb=" CB THR Z 206 " pdb=" CA THR Z 206 " pdb=" OG1 THR Z 206 " pdb=" CG2 THR Z 206 " both_signs ideal model delta sigma weight residual False 2.55 2.38 0.17 2.00e-01 2.50e+01 7.36e-01 ... (remaining 964 not shown) Planarity restraints: 1045 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU H 189 " 0.029 5.00e-02 4.00e+02 4.42e-02 3.12e+00 pdb=" N PRO H 190 " -0.076 5.00e-02 4.00e+02 pdb=" CA PRO H 190 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO H 190 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL H 135 " -0.008 2.00e-02 2.50e+03 1.64e-02 2.70e+00 pdb=" C VAL H 135 " 0.028 2.00e-02 2.50e+03 pdb=" O VAL H 135 " -0.011 2.00e-02 2.50e+03 pdb=" N GLY H 136 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA H 132 " 0.007 2.00e-02 2.50e+03 1.36e-02 1.86e+00 pdb=" C ALA H 132 " -0.024 2.00e-02 2.50e+03 pdb=" O ALA H 132 " 0.009 2.00e-02 2.50e+03 pdb=" N TRP H 133 " 0.008 2.00e-02 2.50e+03 ... (remaining 1042 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 470 2.74 - 3.28: 5767 3.28 - 3.82: 10480 3.82 - 4.36: 12452 4.36 - 4.90: 21514 Nonbonded interactions: 50683 Sorted by model distance: nonbonded pdb=" O SER H 81 " pdb=" OG SER H 81 " model vdw 2.195 3.040 nonbonded pdb=" OD2 ASP L 194 " pdb=" OG1 THR L 196 " model vdw 2.231 3.040 nonbonded pdb=" O SER H 111 " pdb=" OG SER H 111 " model vdw 2.243 3.040 nonbonded pdb=" OG SER Z 81 " pdb=" O SER Z 97 " model vdw 2.276 3.040 nonbonded pdb=" O SER L 54 " pdb=" NH2 ARG L 90 " model vdw 2.290 3.120 ... (remaining 50678 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=0.12 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: 2.770 Set stop_for_unknowns flag: 0.010 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.040 Construct map_model_manager: 0.010 Extract box with map and model: 0.270 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 19.650 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.040 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:12.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 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 : 0.004 0.040 6207 Z= 0.271 Angle : 0.586 8.558 8421 Z= 0.305 Chirality : 0.043 0.215 967 Planarity : 0.004 0.044 1045 Dihedral : 17.050 89.284 2165 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 4.35 % Allowed : 24.02 % Favored : 71.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % 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: 1.63 (0.31), residues: 780 helix: 2.26 (0.29), residues: 343 sheet: 1.21 (0.36), residues: 207 loop : -0.92 (0.40), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 139 HIS 0.002 0.001 HIS H 241 PHE 0.021 0.002 PHE Z 335 TYR 0.011 0.002 TYR H 121 ARG 0.002 0.000 ARG H 64 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 76 time to evaluate : 0.698 Fit side-chains REVERT: L 48 ARG cc_start: 0.7132 (mpt90) cc_final: 0.6915 (mmt180) outliers start: 29 outliers final: 28 residues processed: 103 average time/residue: 1.0112 time to fit residues: 110.2458 Evaluate side-chains 102 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 74 time to evaluate : 0.736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Z residue 5 ILE Chi-restraints excluded: chain Z residue 26 LEU Chi-restraints excluded: chain Z residue 79 SER Chi-restraints excluded: chain Z residue 153 VAL Chi-restraints excluded: chain Z residue 206 THR Chi-restraints excluded: chain Z residue 209 ILE Chi-restraints excluded: chain Z residue 229 THR Chi-restraints excluded: chain Z residue 267 SER Chi-restraints excluded: chain Z residue 309 ILE Chi-restraints excluded: chain Z residue 353 VAL Chi-restraints excluded: chain H residue 28 VAL Chi-restraints excluded: chain H residue 38 VAL Chi-restraints excluded: chain H residue 58 SER Chi-restraints excluded: chain H residue 74 VAL Chi-restraints excluded: chain H residue 81 SER Chi-restraints excluded: chain H residue 90 VAL Chi-restraints excluded: chain H residue 101 SER Chi-restraints excluded: chain H residue 117 THR Chi-restraints excluded: chain H residue 152 THR Chi-restraints excluded: chain H residue 191 VAL Chi-restraints excluded: chain L residue 54 SER Chi-restraints excluded: chain L residue 57 VAL Chi-restraints excluded: chain L residue 96 THR Chi-restraints excluded: chain L residue 118 SER Chi-restraints excluded: chain L residue 124 GLN Chi-restraints excluded: chain L residue 155 SER Chi-restraints excluded: chain L residue 159 LEU Chi-restraints excluded: chain L residue 200 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 66 optimal weight: 0.2980 chunk 59 optimal weight: 0.0060 chunk 33 optimal weight: 0.9980 chunk 20 optimal weight: 1.9990 chunk 40 optimal weight: 3.9990 chunk 31 optimal weight: 0.8980 chunk 61 optimal weight: 0.4980 chunk 23 optimal weight: 1.9990 chunk 37 optimal weight: 3.9990 chunk 46 optimal weight: 0.8980 chunk 71 optimal weight: 5.9990 overall best weight: 0.5196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Z 128 ASN ** H 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.163638 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.118203 restraints weight = 7890.294| |-----------------------------------------------------------------------------| r_work (start): 0.3365 rms_B_bonded: 2.36 r_work: 0.3137 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3012 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.3012 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3011 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3011 r_free = 0.3011 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.12 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3010 r_free = 0.3010 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3010 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8412 moved from start: 0.0621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6207 Z= 0.184 Angle : 0.545 8.368 8421 Z= 0.284 Chirality : 0.041 0.169 967 Planarity : 0.004 0.044 1045 Dihedral : 7.068 54.707 879 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 3.60 % Allowed : 22.67 % Favored : 73.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % 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: 1.94 (0.31), residues: 780 helix: 2.55 (0.29), residues: 345 sheet: 1.46 (0.37), residues: 197 loop : -0.85 (0.39), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 133 HIS 0.003 0.001 HIS Z 155 PHE 0.015 0.001 PHE Z 335 TYR 0.009 0.001 TYR H 121 ARG 0.002 0.000 ARG H 134 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 72 time to evaluate : 0.558 Fit side-chains REVERT: L 48 ARG cc_start: 0.7528 (mpt90) cc_final: 0.7180 (mmt180) outliers start: 24 outliers final: 11 residues processed: 93 average time/residue: 1.1702 time to fit residues: 114.4694 Evaluate side-chains 82 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 71 time to evaluate : 0.709 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Z residue 153 VAL Chi-restraints excluded: chain Z residue 309 ILE Chi-restraints excluded: chain Z residue 353 VAL Chi-restraints excluded: chain H residue 28 VAL Chi-restraints excluded: chain H residue 74 VAL Chi-restraints excluded: chain H residue 90 VAL Chi-restraints excluded: chain H residue 152 THR Chi-restraints excluded: chain H residue 191 VAL Chi-restraints excluded: chain H residue 253 GLU Chi-restraints excluded: chain L residue 57 VAL Chi-restraints excluded: chain L residue 145 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 42 optimal weight: 0.1980 chunk 30 optimal weight: 0.9990 chunk 23 optimal weight: 0.8980 chunk 35 optimal weight: 0.9980 chunk 17 optimal weight: 0.7980 chunk 37 optimal weight: 0.4980 chunk 18 optimal weight: 4.9990 chunk 1 optimal weight: 0.0980 chunk 33 optimal weight: 0.3980 chunk 3 optimal weight: 4.9990 chunk 64 optimal weight: 2.9990 overall best weight: 0.3980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.165076 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.119718 restraints weight = 7895.771| |-----------------------------------------------------------------------------| r_work (start): 0.3392 rms_B_bonded: 2.31 r_work: 0.3162 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3036 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.3036 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3033 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3033 r_free = 0.3033 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3033 r_free = 0.3033 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3033 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8391 moved from start: 0.0907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 6207 Z= 0.163 Angle : 0.519 6.375 8421 Z= 0.270 Chirality : 0.040 0.168 967 Planarity : 0.004 0.043 1045 Dihedral : 5.528 55.922 854 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 3.15 % Allowed : 22.97 % Favored : 73.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.03 (0.31), residues: 780 helix: 2.62 (0.29), residues: 346 sheet: 1.50 (0.37), residues: 197 loop : -0.82 (0.39), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 133 HIS 0.003 0.001 HIS Z 155 PHE 0.014 0.001 PHE Z 16 TYR 0.009 0.001 TYR H 121 ARG 0.002 0.000 ARG H 134 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 81 time to evaluate : 0.675 Fit side-chains REVERT: Z 269 LEU cc_start: 0.8225 (mt) cc_final: 0.8013 (mm) REVERT: H 91 LYS cc_start: 0.7835 (OUTLIER) cc_final: 0.7463 (tmtt) REVERT: H 154 PHE cc_start: 0.6426 (m-80) cc_final: 0.6053 (m-10) REVERT: L 48 ARG cc_start: 0.7490 (mpt90) cc_final: 0.6851 (mmt90) REVERT: L 199 LEU cc_start: 0.8056 (tt) cc_final: 0.7735 (tm) outliers start: 21 outliers final: 10 residues processed: 96 average time/residue: 1.1400 time to fit residues: 115.4778 Evaluate side-chains 88 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 77 time to evaluate : 0.701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Z residue 17 LEU Chi-restraints excluded: chain Z residue 202 LYS Chi-restraints excluded: chain Z residue 206 THR Chi-restraints excluded: chain Z residue 353 VAL Chi-restraints excluded: chain H residue 28 VAL Chi-restraints excluded: chain H residue 74 VAL Chi-restraints excluded: chain H residue 90 VAL Chi-restraints excluded: chain H residue 91 LYS Chi-restraints excluded: chain H residue 191 VAL Chi-restraints excluded: chain L residue 57 VAL Chi-restraints excluded: chain L residue 145 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 65.7564 > 50: distance: 7 - 9: 27.245 distance: 9 - 10: 17.893 distance: 10 - 11: 4.576 distance: 11 - 12: 5.627 distance: 11 - 13: 5.287 distance: 13 - 14: 17.248 distance: 14 - 15: 21.272 distance: 14 - 17: 25.345 distance: 15 - 16: 14.700 distance: 15 - 21: 16.279 distance: 17 - 18: 28.416 distance: 18 - 19: 32.452 distance: 18 - 20: 27.720 distance: 21 - 22: 33.815 distance: 22 - 23: 8.001 distance: 22 - 25: 27.236 distance: 23 - 24: 11.459 distance: 23 - 28: 57.279 distance: 25 - 26: 22.332 distance: 25 - 27: 49.656 distance: 28 - 29: 27.037 distance: 29 - 32: 33.023 distance: 30 - 31: 17.023 distance: 32 - 33: 19.517 distance: 34 - 35: 41.209 distance: 34 - 36: 19.321 distance: 37 - 38: 43.837 distance: 37 - 43: 46.438 distance: 38 - 41: 3.396 distance: 41 - 42: 54.327 distance: 42 - 43: 33.735 distance: 45 - 46: 3.780 distance: 46 - 47: 35.915 distance: 46 - 48: 5.236 distance: 48 - 49: 7.732 distance: 49 - 50: 9.888 distance: 50 - 52: 6.392 distance: 52 - 53: 22.910 distance: 53 - 54: 6.984 distance: 53 - 56: 16.684 distance: 54 - 55: 18.168 distance: 54 - 58: 7.552 distance: 58 - 59: 22.388 distance: 58 - 107: 19.088 distance: 59 - 60: 22.142 distance: 59 - 62: 20.031 distance: 60 - 61: 19.290 distance: 60 - 66: 20.709 distance: 61 - 104: 37.392 distance: 62 - 63: 34.926 distance: 63 - 65: 40.591 distance: 66 - 67: 15.192 distance: 67 - 68: 15.222 distance: 67 - 70: 34.104 distance: 68 - 69: 31.862 distance: 68 - 77: 14.338 distance: 70 - 71: 56.682 distance: 71 - 72: 38.890 distance: 72 - 73: 46.197 distance: 73 - 74: 12.626 distance: 74 - 75: 14.259 distance: 74 - 76: 22.043