Starting phenix.real_space_refine on Fri Aug 2 20:33:23 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xlt_33286/08_2024/7xlt_33286.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xlt_33286/08_2024/7xlt_33286.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xlt_33286/08_2024/7xlt_33286.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xlt_33286/08_2024/7xlt_33286.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xlt_33286/08_2024/7xlt_33286.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xlt_33286/08_2024/7xlt_33286.cif" } resolution = 4.4 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= -0.001 sd= 0.046 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 78 5.49 5 S 14 5.16 5 C 2869 2.51 5 N 845 2.21 5 O 1179 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "H ASP 73": "OD1" <-> "OD2" Residue "H ASP 107": "OD1" <-> "OD2" Residue "H TYR 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 39": "OE1" <-> "OE2" Residue "L TYR 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 75": "OD1" <-> "OD2" Residue "L PHE 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 148": "OD1" <-> "OD2" Residue "L GLU 200": "OE1" <-> "OE2" Residue "L PHE 214": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 4985 Number of models: 1 Model: "" Number of chains: 4 Chain: "H" Number of atoms: 1635 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1635 Classifications: {'peptide': 215} Link IDs: {'PTRANS': 11, 'TRANS': 203} Chain: "L" Number of atoms: 1676 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1676 Classifications: {'peptide': 216} Link IDs: {'PTRANS': 11, 'TRANS': 204} Chain: "A" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 801 Classifications: {'DNA': 40} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 39} Chain: "B" Number of atoms: 873 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 873 Classifications: {'RNA': 40} Modifications used: {'5*END': 1, 'rna3p_pur': 32, 'rna3p_pyr': 8} Link IDs: {'rna3p': 39} Time building chain proxies: 3.75, per 1000 atoms: 0.75 Number of scatterers: 4985 At special positions: 0 Unit cell: (125.465, 106.918, 93.826, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 14 16.00 P 78 15.00 O 1179 8.00 N 845 7.00 C 2869 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 146 " - pdb=" SG CYS H 201 " distance=2.04 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 93 " distance=2.04 Simple disulfide: pdb=" SG CYS L 139 " - pdb=" SG CYS L 199 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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: 2.43 Conformation dependent library (CDL) restraints added in 810.8 milliseconds 854 Ramachandran restraints generated. 427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 796 Finding SS restraints... Secondary structure from input PDB file: 5 helices and 9 sheets defined 5.6% alpha, 36.0% beta 41 base pairs and 55 stacking pairs defined. Time for finding SS restraints: 2.13 Creating SS restraints... Processing helix chain 'H' and resid 87 through 91 removed outlier: 3.606A pdb=" N ASP H 90 " --> pdb=" O THR H 87 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N SER H 91 " --> pdb=" O SER H 88 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 87 through 91' Processing helix chain 'H' and resid 176 through 180 Processing helix chain 'H' and resid 192 through 194 No H-bonds generated for 'chain 'H' and resid 192 through 194' Processing helix chain 'L' and resid 126 through 131 Processing helix chain 'L' and resid 188 through 192 Processing sheet with id=AA1, first strand: chain 'H' and resid 4 through 6 Processing sheet with id=AA2, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.340A pdb=" N GLU H 10 " --> pdb=" O THR H 116 " (cutoff:3.500A) removed outlier: 5.750A pdb=" N VAL H 33 " --> pdb=" O ASP H 99 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N MET H 34 " --> pdb=" O PHE H 50 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N PHE H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.340A pdb=" N GLU H 10 " --> pdb=" O THR H 116 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N TYR H 108 " --> pdb=" O ARG H 98 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 126 through 129 removed outlier: 3.988A pdb=" N SER H 186 " --> pdb=" O HIS H 170 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 157 through 160 Processing sheet with id=AA6, first strand: chain 'L' and resid 4 through 6 Processing sheet with id=AA7, first strand: chain 'L' and resid 50 through 53 removed outlier: 5.817A pdb=" N LEU L 51 " --> pdb=" O LEU L 42 " (cutoff:3.500A) removed outlier: 6.078A pdb=" N LEU L 42 " --> pdb=" O LEU L 51 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N THR L 107 " --> pdb=" O TYR L 91 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N CYS L 93 " --> pdb=" O GLY L 105 " (cutoff:3.500A) removed outlier: 5.310A pdb=" N GLY L 105 " --> pdb=" O CYS L 93 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'L' and resid 119 through 123 Processing sheet with id=AA9, first strand: chain 'L' and resid 150 through 155 108 hydrogen bonds defined for protein. 264 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 102 hydrogen bonds 200 hydrogen bond angles 0 basepair planarities 41 basepair parallelities 55 stacking parallelities Total time for adding SS restraints: 1.56 Time building geometry restraints manager: 2.68 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: 1253 1.34 - 1.46: 1731 1.46 - 1.58: 2107 1.58 - 1.70: 156 1.70 - 1.82: 19 Bond restraints: 5266 Sorted by residual: bond pdb=" CA VAL L 99 " pdb=" CB VAL L 99 " ideal model delta sigma weight residual 1.534 1.551 -0.017 6.80e-03 2.16e+04 6.17e+00 bond pdb=" C GLU H 154 " pdb=" N PRO H 155 " ideal model delta sigma weight residual 1.334 1.386 -0.052 2.34e-02 1.83e+03 5.02e+00 bond pdb=" C VAL L 99 " pdb=" N PRO L 100 " ideal model delta sigma weight residual 1.334 1.386 -0.052 2.34e-02 1.83e+03 5.00e+00 bond pdb=" CA VAL L 99 " pdb=" C VAL L 99 " ideal model delta sigma weight residual 1.520 1.539 -0.019 8.80e-03 1.29e+04 4.68e+00 bond pdb=" O5' C B 10 " pdb=" C5' C B 10 " ideal model delta sigma weight residual 1.420 1.452 -0.032 1.50e-02 4.44e+03 4.65e+00 ... (remaining 5261 not shown) Histogram of bond angle deviations from ideal: 97.00 - 104.51: 392 104.51 - 112.02: 2702 112.02 - 119.54: 1788 119.54 - 127.05: 2408 127.05 - 134.56: 230 Bond angle restraints: 7520 Sorted by residual: angle pdb=" C HIS L 98 " pdb=" N VAL L 99 " pdb=" CA VAL L 99 " ideal model delta sigma weight residual 120.24 123.82 -3.58 6.30e-01 2.52e+00 3.22e+01 angle pdb=" C PRO H 153 " pdb=" N GLU H 154 " pdb=" CA GLU H 154 " ideal model delta sigma weight residual 120.09 125.72 -5.63 1.25e+00 6.40e-01 2.03e+01 angle pdb=" CA VAL L 99 " pdb=" C VAL L 99 " pdb=" N PRO L 100 " ideal model delta sigma weight residual 121.00 123.99 -2.99 8.30e-01 1.45e+00 1.30e+01 angle pdb=" CA GLU H 82 " pdb=" CB GLU H 82 " pdb=" CG GLU H 82 " ideal model delta sigma weight residual 114.10 121.30 -7.20 2.00e+00 2.50e-01 1.30e+01 angle pdb=" CB MET L 180 " pdb=" CG MET L 180 " pdb=" SD MET L 180 " ideal model delta sigma weight residual 112.70 123.06 -10.36 3.00e+00 1.11e-01 1.19e+01 ... (remaining 7515 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.74: 2374 15.74 - 31.49: 398 31.49 - 47.23: 133 47.23 - 62.97: 53 62.97 - 78.72: 33 Dihedral angle restraints: 2991 sinusoidal: 1743 harmonic: 1248 Sorted by residual: dihedral pdb=" CA ASN L 58 " pdb=" C ASN L 58 " pdb=" N ARG L 59 " pdb=" CA ARG L 59 " ideal model delta harmonic sigma weight residual 180.00 -155.04 -24.96 0 5.00e+00 4.00e-02 2.49e+01 dihedral pdb=" CA VAL H 156 " pdb=" C VAL H 156 " pdb=" N THR H 157 " pdb=" CA THR H 157 " ideal model delta harmonic sigma weight residual 180.00 -155.62 -24.38 0 5.00e+00 4.00e-02 2.38e+01 dihedral pdb=" CA TYR H 80 " pdb=" C TYR H 80 " pdb=" N MET H 81 " pdb=" CA MET H 81 " ideal model delta harmonic sigma weight residual 180.00 157.33 22.67 0 5.00e+00 4.00e-02 2.06e+01 ... (remaining 2988 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.086: 807 0.086 - 0.172: 59 0.172 - 0.258: 4 0.258 - 0.344: 3 0.344 - 0.430: 1 Chirality restraints: 874 Sorted by residual: chirality pdb=" P C B 37 " pdb=" OP1 C B 37 " pdb=" OP2 C B 37 " pdb=" O5' C B 37 " both_signs ideal model delta sigma weight residual True 2.41 -2.84 -0.43 2.00e-01 2.50e+01 4.62e+00 chirality pdb=" CB ILE L 155 " pdb=" CA ILE L 155 " pdb=" CG1 ILE L 155 " pdb=" CG2 ILE L 155 " both_signs ideal model delta sigma weight residual False 2.64 2.34 0.31 2.00e-01 2.50e+01 2.36e+00 chirality pdb=" P C B 10 " pdb=" OP1 C B 10 " pdb=" OP2 C B 10 " pdb=" O5' C B 10 " both_signs ideal model delta sigma weight residual True 2.41 -2.71 -0.30 2.00e-01 2.50e+01 2.30e+00 ... (remaining 871 not shown) Planarity restraints: 662 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR L 7 " -0.036 5.00e-02 4.00e+02 5.48e-02 4.81e+00 pdb=" N PRO L 8 " 0.095 5.00e-02 4.00e+02 pdb=" CA PRO L 8 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO L 8 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR H 108 " 0.016 2.00e-02 2.50e+03 1.50e-02 4.50e+00 pdb=" CG TYR H 108 " -0.037 2.00e-02 2.50e+03 pdb=" CD1 TYR H 108 " 0.002 2.00e-02 2.50e+03 pdb=" CD2 TYR H 108 " 0.010 2.00e-02 2.50e+03 pdb=" CE1 TYR H 108 " 0.009 2.00e-02 2.50e+03 pdb=" CE2 TYR H 108 " 0.001 2.00e-02 2.50e+03 pdb=" CZ TYR H 108 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR H 108 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP H 107 " -0.009 2.00e-02 2.50e+03 1.92e-02 3.70e+00 pdb=" CG ASP H 107 " 0.033 2.00e-02 2.50e+03 pdb=" OD1 ASP H 107 " -0.012 2.00e-02 2.50e+03 pdb=" OD2 ASP H 107 " -0.012 2.00e-02 2.50e+03 ... (remaining 659 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 1322 2.81 - 3.33: 3795 3.33 - 3.86: 9088 3.86 - 4.38: 9680 4.38 - 4.90: 15108 Nonbonded interactions: 38993 Sorted by model distance: nonbonded pdb=" O GLY H 8 " pdb=" OG1 THR H 113 " model vdw 2.288 3.040 nonbonded pdb=" OG SER H 141 " pdb=" O VAL H 189 " model vdw 2.326 3.040 nonbonded pdb=" OG SER L 57 " pdb=" O GLY L 69 " model vdw 2.337 3.040 nonbonded pdb=" OG SER L 25 " pdb=" O GLN L 27 " model vdw 2.353 3.040 nonbonded pdb=" NH1 ARG L 66 " pdb=" OE2 GLU L 84 " model vdw 2.369 3.120 ... (remaining 38988 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 0.480 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.130 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 21.710 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.020 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:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5953 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 0.052 5266 Z= 0.259 Angle : 0.887 10.357 7520 Z= 0.482 Chirality : 0.050 0.430 874 Planarity : 0.006 0.055 662 Dihedral : 18.802 78.716 2183 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.79 % Favored : 93.21 % Rotamer: Outliers : 0.79 % Allowed : 34.30 % Favored : 64.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.19 (0.39), residues: 427 helix: -3.85 (0.81), residues: 12 sheet: 0.01 (0.39), residues: 188 loop : -2.75 (0.37), residues: 227 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.003 TRP L 168 HIS 0.012 0.002 HIS H 35 PHE 0.024 0.002 PHE L 94 TYR 0.037 0.002 TYR H 108 ARG 0.009 0.001 ARG L 66 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 854 Ramachandran restraints generated. 427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 854 Ramachandran restraints generated. 427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 379 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 70 time to evaluate : 0.441 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 107 THR cc_start: 0.6878 (m) cc_final: 0.6517 (m) REVERT: L 144 PHE cc_start: 0.6641 (m-10) cc_final: 0.6319 (m-10) REVERT: L 171 GLN cc_start: 0.6884 (tp40) cc_final: 0.6116 (tp-100) outliers start: 3 outliers final: 1 residues processed: 71 average time/residue: 0.1815 time to fit residues: 16.2508 Evaluate side-chains 62 residues out of total 379 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 61 time to evaluate : 0.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 42 optimal weight: 20.0000 chunk 37 optimal weight: 6.9990 chunk 21 optimal weight: 8.9990 chunk 12 optimal weight: 9.9990 chunk 25 optimal weight: 4.9990 chunk 20 optimal weight: 6.9990 chunk 39 optimal weight: 5.9990 chunk 15 optimal weight: 3.9990 chunk 23 optimal weight: 7.9990 chunk 29 optimal weight: 9.9990 chunk 45 optimal weight: 10.0000 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 39 GLN H 202 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6399 moved from start: 0.3081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.069 5266 Z= 0.410 Angle : 0.821 9.076 7520 Z= 0.438 Chirality : 0.042 0.179 874 Planarity : 0.006 0.064 662 Dihedral : 16.760 74.066 1436 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 24.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.90 % Favored : 91.10 % Rotamer: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.62 (0.38), residues: 427 helix: -3.79 (0.68), residues: 19 sheet: -0.50 (0.38), residues: 177 loop : -2.68 (0.37), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.004 TRP H 105 HIS 0.006 0.002 HIS H 35 PHE 0.030 0.003 PHE L 76 TYR 0.019 0.003 TYR L 91 ARG 0.007 0.001 ARG L 59 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 854 Ramachandran restraints generated. 427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 854 Ramachandran restraints generated. 427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 379 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 61 time to evaluate : 0.416 Fit side-chains revert: symmetry clash REVERT: L 78 LEU cc_start: 0.8120 (tt) cc_final: 0.7874 (tt) REVERT: L 92 TYR cc_start: 0.6811 (m-10) cc_final: 0.6459 (m-10) REVERT: L 103 PHE cc_start: 0.8064 (t80) cc_final: 0.7702 (t80) REVERT: L 144 PHE cc_start: 0.6485 (m-10) cc_final: 0.6060 (m-10) REVERT: L 149 ILE cc_start: 0.7023 (mm) cc_final: 0.6713 (mm) REVERT: L 180 MET cc_start: 0.7838 (mmm) cc_final: 0.7553 (mmm) outliers start: 0 outliers final: 0 residues processed: 61 average time/residue: 0.1712 time to fit residues: 13.4712 Evaluate side-chains 45 residues out of total 379 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 45 time to evaluate : 0.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 25 optimal weight: 1.9990 chunk 14 optimal weight: 6.9990 chunk 37 optimal weight: 5.9990 chunk 30 optimal weight: 1.9990 chunk 12 optimal weight: 7.9990 chunk 45 optimal weight: 10.0000 chunk 49 optimal weight: 30.0000 chunk 40 optimal weight: 1.9990 chunk 15 optimal weight: 0.9980 chunk 36 optimal weight: 6.9990 chunk 44 optimal weight: 10.0000 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6314 moved from start: 0.3266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 5266 Z= 0.223 Angle : 0.661 7.107 7520 Z= 0.356 Chirality : 0.037 0.158 874 Planarity : 0.005 0.047 662 Dihedral : 16.724 73.895 1436 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 20.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.32 % Favored : 93.68 % Rotamer: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.44 (0.38), residues: 427 helix: -3.45 (0.84), residues: 19 sheet: -0.17 (0.39), residues: 168 loop : -2.68 (0.36), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP H 47 HIS 0.006 0.001 HIS H 35 PHE 0.013 0.001 PHE L 76 TYR 0.013 0.002 TYR H 54 ARG 0.004 0.001 ARG L 59 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 854 Ramachandran restraints generated. 427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 854 Ramachandran restraints generated. 427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 379 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 55 time to evaluate : 0.436 Fit side-chains revert: symmetry clash REVERT: H 45 LEU cc_start: 0.7930 (mm) cc_final: 0.7725 (mt) REVERT: L 92 TYR cc_start: 0.6904 (m-10) cc_final: 0.6614 (m-10) REVERT: L 103 PHE cc_start: 0.7919 (t80) cc_final: 0.7460 (t80) REVERT: L 144 PHE cc_start: 0.6429 (m-10) cc_final: 0.6058 (m-10) REVERT: L 149 ILE cc_start: 0.6576 (mm) cc_final: 0.6245 (mm) REVERT: L 180 MET cc_start: 0.7412 (mmm) cc_final: 0.7197 (mmm) outliers start: 0 outliers final: 0 residues processed: 55 average time/residue: 0.1710 time to fit residues: 12.2546 Evaluate side-chains 46 residues out of total 379 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 46 time to evaluate : 0.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 34 optimal weight: 9.9990 chunk 23 optimal weight: 10.0000 chunk 5 optimal weight: 5.9990 chunk 21 optimal weight: 4.9990 chunk 30 optimal weight: 5.9990 chunk 45 optimal weight: 10.0000 chunk 48 optimal weight: 10.0000 chunk 43 optimal weight: 8.9990 chunk 13 optimal weight: 0.8980 chunk 40 optimal weight: 5.9990 chunk 27 optimal weight: 10.0000 overall best weight: 4.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 129 GLN L 166 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6550 moved from start: 0.4250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 5266 Z= 0.346 Angle : 0.785 10.388 7520 Z= 0.419 Chirality : 0.042 0.176 874 Planarity : 0.006 0.044 662 Dihedral : 17.053 74.203 1436 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 28.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.13 % Favored : 90.87 % Rotamer: Outliers : 0.26 % Allowed : 7.65 % Favored : 92.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.62 (0.39), residues: 427 helix: -3.23 (0.82), residues: 19 sheet: -0.56 (0.41), residues: 167 loop : -2.60 (0.38), residues: 241 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.003 TRP H 109 HIS 0.003 0.001 HIS H 205 PHE 0.040 0.003 PHE L 76 TYR 0.018 0.002 TYR L 191 ARG 0.006 0.001 ARG L 59 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 854 Ramachandran restraints generated. 427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 854 Ramachandran restraints generated. 427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 379 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 47 time to evaluate : 0.458 Fit side-chains revert: symmetry clash REVERT: L 144 PHE cc_start: 0.6623 (m-10) cc_final: 0.6350 (m-10) REVERT: L 149 ILE cc_start: 0.6830 (mm) cc_final: 0.6364 (mm) outliers start: 1 outliers final: 1 residues processed: 48 average time/residue: 0.1936 time to fit residues: 12.6580 Evaluate side-chains 43 residues out of total 379 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 42 time to evaluate : 0.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 0 optimal weight: 10.0000 chunk 35 optimal weight: 9.9990 chunk 19 optimal weight: 10.0000 chunk 41 optimal weight: 20.0000 chunk 33 optimal weight: 20.0000 chunk 24 optimal weight: 3.9990 chunk 43 optimal weight: 8.9990 chunk 12 optimal weight: 5.9990 chunk 16 optimal weight: 20.0000 chunk 9 optimal weight: 7.9990 chunk 28 optimal weight: 2.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6599 moved from start: 0.4815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.058 5266 Z= 0.406 Angle : 0.820 7.609 7520 Z= 0.440 Chirality : 0.043 0.182 874 Planarity : 0.006 0.049 662 Dihedral : 17.317 74.310 1436 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 31.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.13 % Favored : 90.87 % Rotamer: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.93 (0.39), residues: 427 helix: -3.99 (0.68), residues: 19 sheet: -0.61 (0.40), residues: 170 loop : -2.92 (0.37), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.003 TRP H 47 HIS 0.008 0.002 HIS H 35 PHE 0.024 0.003 PHE L 76 TYR 0.023 0.003 TYR H 27 ARG 0.011 0.002 ARG H 98 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 854 Ramachandran restraints generated. 427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 854 Ramachandran restraints generated. 427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 379 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 52 time to evaluate : 0.590 Fit side-chains REVERT: L 144 PHE cc_start: 0.6699 (m-10) cc_final: 0.6326 (m-10) REVERT: L 149 ILE cc_start: 0.6947 (mm) cc_final: 0.6430 (mm) REVERT: L 181 SER cc_start: 0.6661 (t) cc_final: 0.6162 (m) REVERT: L 192 GLU cc_start: 0.6741 (mp0) cc_final: 0.5993 (tp30) outliers start: 0 outliers final: 0 residues processed: 52 average time/residue: 0.2018 time to fit residues: 13.7953 Evaluate side-chains 43 residues out of total 379 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 43 time to evaluate : 0.787 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 11 optimal weight: 0.8980 chunk 48 optimal weight: 10.0000 chunk 40 optimal weight: 6.9990 chunk 22 optimal weight: 7.9990 chunk 4 optimal weight: 0.9980 chunk 16 optimal weight: 20.0000 chunk 25 optimal weight: 1.9990 chunk 46 optimal weight: 30.0000 chunk 5 optimal weight: 0.4980 chunk 27 optimal weight: 9.9990 chunk 35 optimal weight: 9.9990 overall best weight: 2.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6434 moved from start: 0.4635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 5266 Z= 0.220 Angle : 0.684 6.380 7520 Z= 0.371 Chirality : 0.039 0.158 874 Planarity : 0.005 0.050 662 Dihedral : 17.106 73.898 1436 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 20.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.73 % Favored : 92.27 % Rotamer: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.65 (0.40), residues: 427 helix: -3.76 (0.78), residues: 19 sheet: -0.34 (0.40), residues: 169 loop : -2.80 (0.38), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.003 TRP H 47 HIS 0.003 0.001 HIS H 35 PHE 0.020 0.002 PHE L 76 TYR 0.021 0.002 TYR L 191 ARG 0.005 0.001 ARG H 98 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 854 Ramachandran restraints generated. 427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 854 Ramachandran restraints generated. 427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 379 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 55 time to evaluate : 0.421 Fit side-chains REVERT: L 103 PHE cc_start: 0.8165 (t80) cc_final: 0.7936 (t80) REVERT: L 144 PHE cc_start: 0.6493 (m-10) cc_final: 0.6197 (m-10) REVERT: L 149 ILE cc_start: 0.6801 (mm) cc_final: 0.6311 (mm) outliers start: 0 outliers final: 0 residues processed: 55 average time/residue: 0.1462 time to fit residues: 10.8218 Evaluate side-chains 47 residues out of total 379 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 47 time to evaluate : 0.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 27 optimal weight: 0.6980 chunk 40 optimal weight: 5.9990 chunk 48 optimal weight: 9.9990 chunk 30 optimal weight: 4.9990 chunk 29 optimal weight: 3.9990 chunk 22 optimal weight: 8.9990 chunk 19 optimal weight: 7.9990 chunk 28 optimal weight: 0.8980 chunk 14 optimal weight: 20.0000 chunk 9 optimal weight: 6.9990 chunk 32 optimal weight: 8.9990 overall best weight: 3.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6493 moved from start: 0.4946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 5266 Z= 0.265 Angle : 0.707 9.145 7520 Z= 0.379 Chirality : 0.040 0.248 874 Planarity : 0.005 0.050 662 Dihedral : 17.053 73.979 1436 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 24.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.13 % Favored : 90.87 % Rotamer: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.37 (0.41), residues: 427 helix: -3.17 (1.09), residues: 12 sheet: -0.45 (0.40), residues: 172 loop : -2.45 (0.40), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP H 36 HIS 0.004 0.001 HIS H 35 PHE 0.021 0.002 PHE L 76 TYR 0.013 0.002 TYR H 27 ARG 0.002 0.001 ARG H 98 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 854 Ramachandran restraints generated. 427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 854 Ramachandran restraints generated. 427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 379 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 50 time to evaluate : 0.414 Fit side-chains REVERT: L 4 MET cc_start: 0.8698 (tmm) cc_final: 0.8367 (tmm) outliers start: 0 outliers final: 0 residues processed: 50 average time/residue: 0.1533 time to fit residues: 10.2468 Evaluate side-chains 43 residues out of total 379 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 43 time to evaluate : 0.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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-5409/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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-5409/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-5409/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-5409/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-5409/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-5409/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-5409/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-5409/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-5409/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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-5409/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-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 71.2941 > 50: distance: 4 - 9: 30.742 distance: 9 - 10: 24.620 distance: 10 - 11: 42.092 distance: 10 - 13: 7.681 distance: 11 - 12: 22.050 distance: 11 - 17: 17.341 distance: 13 - 14: 61.879 distance: 14 - 15: 39.031 distance: 14 - 16: 40.333 distance: 17 - 18: 39.024 distance: 18 - 19: 34.155 distance: 18 - 21: 14.208 distance: 19 - 20: 56.200 distance: 19 - 22: 50.453 distance: 22 - 23: 35.430 distance: 22 - 28: 9.100 distance: 23 - 24: 39.403 distance: 23 - 26: 40.484 distance: 24 - 25: 39.577 distance: 24 - 29: 43.434 distance: 26 - 27: 29.443 distance: 27 - 28: 45.864 distance: 29 - 30: 56.110 distance: 30 - 31: 34.655 distance: 30 - 33: 35.495 distance: 31 - 32: 47.882 distance: 31 - 36: 40.761 distance: 33 - 34: 66.780 distance: 33 - 35: 42.974 distance: 36 - 37: 69.542 distance: 37 - 40: 70.489 distance: 38 - 39: 56.617 distance: 38 - 42: 40.819 distance: 40 - 41: 42.697 distance: 42 - 43: 56.518 distance: 43 - 44: 68.399 distance: 44 - 45: 40.249 distance: 44 - 46: 40.079 distance: 46 - 47: 10.966 distance: 47 - 48: 52.000 distance: 47 - 50: 27.221 distance: 48 - 49: 17.610 distance: 48 - 54: 42.744 distance: 50 - 51: 56.334 distance: 51 - 52: 56.492 distance: 51 - 53: 56.731 distance: 54 - 55: 9.560 distance: 55 - 56: 29.460 distance: 55 - 58: 29.923 distance: 56 - 61: 54.902 distance: 58 - 59: 58.907 distance: 58 - 60: 55.475 distance: 61 - 62: 28.404 distance: 62 - 63: 52.309 distance: 62 - 65: 26.365 distance: 63 - 64: 17.372 distance: 63 - 68: 25.565 distance: 65 - 66: 33.151 distance: 65 - 67: 42.295 distance: 68 - 69: 15.032 distance: 69 - 70: 21.991 distance: 70 - 71: 19.755 distance: 70 - 72: 20.825