Starting phenix.real_space_refine on Mon Jan 13 13:36:45 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8az0_15728/01_2025/8az0_15728.cif Found real_map, /net/cci-nas-00/data/ceres_data/8az0_15728/01_2025/8az0_15728.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8az0_15728/01_2025/8az0_15728.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8az0_15728/01_2025/8az0_15728.map" model { file = "/net/cci-nas-00/data/ceres_data/8az0_15728/01_2025/8az0_15728.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8az0_15728/01_2025/8az0_15728.cif" } resolution = 3.4 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= 0.000 sd= 0.003 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: 3 Type Number sf(0) Gaussians C 1350 2.51 5 N 420 2.21 5 O 410 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 30 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 2180 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 217 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 28, 210 Classifications: {'peptide': 28} Link IDs: {'TRANS': 27} Conformer: "B" Number of residues, atoms: 28, 210 Classifications: {'peptide': 28} Link IDs: {'TRANS': 27} bond proxies already assigned to first conformer: 204 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Restraints were copied for chains: C, B, E, D, G, F, I, H, J Time building chain proxies: 1.63, per 1000 atoms: 0.75 Number of scatterers: 2180 At special positions: 0 Unit cell: (63, 73.08, 45.36, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 3 Type Number sf(0) O 410 8.00 N 420 7.00 C 1350 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=10, symmetry=0 Number of additional bonds: simple=10, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.58 Conformation dependent library (CDL) restraints added in 467.7 milliseconds 540 Ramachandran restraints generated. 270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 520 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 6 sheets defined 0.0% alpha, 53.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.31 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 11 through 22 removed outlier: 6.969A pdb=" N ASN A 21 " --> pdb=" O GLY C 20 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N ASN C 22 " --> pdb=" O ASN A 21 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N ASN C 21 " --> pdb=" O GLY E 20 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N ASN E 22 " --> pdb=" O ASN C 21 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N ASN E 21 " --> pdb=" O GLY G 20 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N ASN G 22 " --> pdb=" O ASN E 21 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N ASN G 21 " --> pdb=" O GLY I 20 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N ASN I 22 " --> pdb=" O ASN G 21 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 25 through 26 Processing sheet with id=AA3, first strand: chain 'A' and resid 29 through 32 removed outlier: 6.413A pdb=" N SER A 29 " --> pdb=" O THR C 30 " (cutoff:3.500A) removed outlier: 8.014A pdb=" N VAL C 32 " --> pdb=" O SER A 29 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N ASN A 31 " --> pdb=" O VAL C 32 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N SER C 29 " --> pdb=" O THR E 30 " (cutoff:3.500A) removed outlier: 8.007A pdb=" N VAL E 32 " --> pdb=" O SER C 29 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N ASN C 31 " --> pdb=" O VAL E 32 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N SER E 29 " --> pdb=" O THR G 30 " (cutoff:3.500A) removed outlier: 8.049A pdb=" N VAL G 32 " --> pdb=" O SER E 29 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N ASN E 31 " --> pdb=" O VAL G 32 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N SER G 29 " --> pdb=" O THR I 30 " (cutoff:3.500A) removed outlier: 7.992A pdb=" N VAL I 32 " --> pdb=" O SER G 29 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N ASN G 31 " --> pdb=" O VAL I 32 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'B' and resid 11 through 22 removed outlier: 6.991A pdb=" N ASN B 21 " --> pdb=" O GLY D 20 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N ASN D 22 " --> pdb=" O ASN B 21 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N ASN D 21 " --> pdb=" O GLY F 20 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N ASN F 22 " --> pdb=" O ASN D 21 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N ASN F 21 " --> pdb=" O GLY H 20 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N ASN H 22 " --> pdb=" O ASN F 21 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N ASN H 21 " --> pdb=" O GLY J 20 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N ASN J 22 " --> pdb=" O ASN H 21 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 25 through 26 Processing sheet with id=AA6, first strand: chain 'B' and resid 29 through 32 removed outlier: 6.397A pdb=" N SER B 29 " --> pdb=" O THR D 30 " (cutoff:3.500A) removed outlier: 7.996A pdb=" N VAL D 32 " --> pdb=" O SER B 29 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N ASN B 31 " --> pdb=" O VAL D 32 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N SER D 29 " --> pdb=" O THR F 30 " (cutoff:3.500A) removed outlier: 8.046A pdb=" N VAL F 32 " --> pdb=" O SER D 29 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N ASN D 31 " --> pdb=" O VAL F 32 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N SER F 29 " --> pdb=" O THR H 30 " (cutoff:3.500A) removed outlier: 8.009A pdb=" N VAL H 32 " --> pdb=" O SER F 29 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N ASN F 31 " --> pdb=" O VAL H 32 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N SER H 29 " --> pdb=" O THR J 30 " (cutoff:3.500A) removed outlier: 7.990A pdb=" N VAL J 32 " --> pdb=" O SER H 29 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N ASN H 31 " --> pdb=" O VAL J 32 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 80 hydrogen bonds defined for protein. 232 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.51 Time building geometry restraints manager: 0.68 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.29: 340 1.29 - 1.35: 400 1.35 - 1.41: 270 1.41 - 1.48: 306 1.48 - 1.54: 904 Bond restraints: 2220 Sorted by residual: bond pdb=" N THR G 36 " pdb=" CA THR G 36 " ideal model delta sigma weight residual 1.457 1.487 -0.030 1.26e-02 6.30e+03 5.76e+00 bond pdb=" N THR J 36 " pdb=" CA THR J 36 " ideal model delta sigma weight residual 1.457 1.487 -0.030 1.26e-02 6.30e+03 5.73e+00 bond pdb=" N THR B 36 " pdb=" CA THR B 36 " ideal model delta sigma weight residual 1.457 1.487 -0.030 1.26e-02 6.30e+03 5.68e+00 bond pdb=" N THR H 36 " pdb=" CA THR H 36 " ideal model delta sigma weight residual 1.457 1.487 -0.030 1.26e-02 6.30e+03 5.62e+00 bond pdb=" N THR E 36 " pdb=" CA THR E 36 " ideal model delta sigma weight residual 1.457 1.487 -0.030 1.26e-02 6.30e+03 5.62e+00 ... (remaining 2215 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.92: 2678 0.92 - 1.84: 200 1.84 - 2.76: 102 2.76 - 3.68: 30 3.68 - 4.60: 10 Bond angle restraints: 3020 Sorted by residual: angle pdb=" CA SER B 34 " pdb=" C SER B 34 " pdb=" O SER B 34 " ideal model delta sigma weight residual 121.28 117.78 3.50 1.19e+00 7.06e-01 8.64e+00 angle pdb=" CA SER A 34 " pdb=" C SER A 34 " pdb=" O SER A 34 " ideal model delta sigma weight residual 121.28 117.80 3.48 1.19e+00 7.06e-01 8.57e+00 angle pdb=" CA SER J 34 " pdb=" C SER J 34 " pdb=" O SER J 34 " ideal model delta sigma weight residual 121.28 117.81 3.47 1.19e+00 7.06e-01 8.49e+00 angle pdb=" CA SER G 34 " pdb=" C SER G 34 " pdb=" O SER G 34 " ideal model delta sigma weight residual 121.28 117.81 3.47 1.19e+00 7.06e-01 8.49e+00 angle pdb=" CA SER D 34 " pdb=" C SER D 34 " pdb=" O SER D 34 " ideal model delta sigma weight residual 121.28 117.83 3.45 1.19e+00 7.06e-01 8.42e+00 ... (remaining 3015 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 5.96: 1022 5.96 - 11.92: 128 11.92 - 17.87: 72 17.87 - 23.83: 28 23.83 - 29.79: 10 Dihedral angle restraints: 1260 sinusoidal: 440 harmonic: 820 Sorted by residual: dihedral pdb=" N HIS J 18 " pdb=" CA AHIS J 18 " pdb=" CB AHIS J 18 " pdb=" CG AHIS J 18 " ideal model delta sinusoidal sigma weight residual -60.00 -83.02 23.02 3 1.50e+01 4.44e-03 3.05e+00 dihedral pdb=" N HIS E 18 " pdb=" CA AHIS E 18 " pdb=" CB AHIS E 18 " pdb=" CG AHIS E 18 " ideal model delta sinusoidal sigma weight residual -60.00 -83.00 23.00 3 1.50e+01 4.44e-03 3.04e+00 dihedral pdb=" N HIS D 18 " pdb=" CA AHIS D 18 " pdb=" CB AHIS D 18 " pdb=" CG AHIS D 18 " ideal model delta sinusoidal sigma weight residual -60.00 -82.99 22.99 3 1.50e+01 4.44e-03 3.04e+00 ... (remaining 1257 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 127 0.027 - 0.054: 149 0.054 - 0.080: 24 0.080 - 0.107: 17 0.107 - 0.134: 23 Chirality restraints: 340 Sorted by residual: chirality pdb=" CA ILE F 26 " pdb=" N ILE F 26 " pdb=" C ILE F 26 " pdb=" CB ILE F 26 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.48e-01 chirality pdb=" CA ILE B 26 " pdb=" N ILE B 26 " pdb=" C ILE B 26 " pdb=" CB ILE B 26 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.28e-01 chirality pdb=" CA ILE I 26 " pdb=" N ILE I 26 " pdb=" C ILE I 26 " pdb=" CB ILE I 26 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.24e-01 ... (remaining 337 not shown) Planarity restraints: 400 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL D 32 " -0.015 2.00e-02 2.50e+03 2.96e-02 8.77e+00 pdb=" C VAL D 32 " 0.051 2.00e-02 2.50e+03 pdb=" O VAL D 32 " -0.019 2.00e-02 2.50e+03 pdb=" N GLY D 33 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL B 32 " -0.015 2.00e-02 2.50e+03 2.96e-02 8.76e+00 pdb=" C VAL B 32 " 0.051 2.00e-02 2.50e+03 pdb=" O VAL B 32 " -0.019 2.00e-02 2.50e+03 pdb=" N GLY B 33 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL I 32 " 0.014 2.00e-02 2.50e+03 2.94e-02 8.67e+00 pdb=" C VAL I 32 " -0.051 2.00e-02 2.50e+03 pdb=" O VAL I 32 " 0.019 2.00e-02 2.50e+03 pdb=" N GLY I 33 " 0.017 2.00e-02 2.50e+03 ... (remaining 397 not shown) Histogram of nonbonded interaction distances: 2.61 - 3.07: 1471 3.07 - 3.53: 1993 3.53 - 3.98: 3105 3.98 - 4.44: 3846 4.44 - 4.90: 7332 Nonbonded interactions: 17747 Sorted by model distance: nonbonded pdb=" O SER B 34 " pdb=" OG SER B 34 " model vdw 2.611 3.040 nonbonded pdb=" O SER J 34 " pdb=" OG SER J 34 " model vdw 2.612 3.040 nonbonded pdb=" O SER F 34 " pdb=" OG SER F 34 " model vdw 2.612 3.040 nonbonded pdb=" O SER H 34 " pdb=" OG SER H 34 " model vdw 2.612 3.040 nonbonded pdb=" O SER D 34 " pdb=" OG SER D 34 " model vdw 2.612 3.040 ... (remaining 17742 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' selection = chain 'G' selection = chain 'F' selection = chain 'I' selection = chain 'H' selection = chain 'J' } 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=0.50 max=1.00 mean=0.97 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.210 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.080 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 10.330 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 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 : 0.006 0.032 2220 Z= 0.392 Angle : 0.742 4.601 3020 Z= 0.491 Chirality : 0.051 0.134 340 Planarity : 0.005 0.030 400 Dihedral : 8.049 29.789 740 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 0.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.69 % Favored : 92.31 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.46 (0.25), residues: 270 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.39 (0.19), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.005 0.001 PHE B 23 TYR 0.003 0.001 TYR E 37 ARG 0.000 0.000 ARG E 11 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 540 Ramachandran restraints generated. 270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 540 Ramachandran restraints generated. 270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 13 residues out of total 220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 13 time to evaluate : 0.241 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 13 average time/residue: 0.0725 time to fit residues: 1.5592 Evaluate side-chains 13 residues out of total 220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 13 time to evaluate : 0.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 16 optimal weight: 9.9990 chunk 15 optimal weight: 10.0000 chunk 8 optimal weight: 9.9990 chunk 5 optimal weight: 8.9990 chunk 10 optimal weight: 8.9990 chunk 6 optimal weight: 3.9990 chunk 9 optimal weight: 0.9990 chunk 11 optimal weight: 0.9980 chunk 18 optimal weight: 8.9990 chunk 12 optimal weight: 0.8980 chunk 19 optimal weight: 1.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 18 HIS A A 21 ASN B 18 HIS A B 21 ASN C 18 HIS A C 21 ASN D 18 HIS A D 21 ASN E 18 HIS A E 21 ASN F 18 HIS A F 21 ASN G 18 HIS A G 21 ASN H 18 HIS A H 21 ASN I 18 HIS A I 21 ASN J 18 HIS A J 21 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.106295 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.083600 restraints weight = 17737.879| |-----------------------------------------------------------------------------| r_work (start): 0.3284 rms_B_bonded: 5.05 r_work: 0.3082 rms_B_bonded: 4.59 restraints_weight: 0.5000 r_work (final): 0.3082 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3104 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3104 r_free = 0.3104 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3098 r_free = 0.3098 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3098 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 moved from start: 0.1481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.014 2220 Z= 0.207 Angle : 0.401 3.087 3020 Z= 0.235 Chirality : 0.044 0.125 340 Planarity : 0.002 0.005 400 Dihedral : 3.697 7.604 310 Min Nonbonded Distance : 2.684 Molprobity Statistics. All-atom Clashscore : 0.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 0.00 % Allowed : 0.42 % Favored : 99.58 % 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: -4.57 (0.27), residues: 270 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.47 (0.20), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.009 0.002 PHE H 15 TYR 0.003 0.001 TYR G 37 ARG 0.001 0.000 ARG B 11 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 540 Ramachandran restraints generated. 270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 540 Ramachandran restraints generated. 270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 25 residues out of total 220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 25 time to evaluate : 0.213 Fit side-chains REVERT: G 19 SER cc_start: 0.8679 (t) cc_final: 0.8305 (p) REVERT: H 19 SER cc_start: 0.8639 (t) cc_final: 0.8308 (p) REVERT: I 19 SER cc_start: 0.8919 (t) cc_final: 0.8703 (p) outliers start: 0 outliers final: 0 residues processed: 25 average time/residue: 0.0669 time to fit residues: 2.4744 Evaluate side-chains 25 residues out of total 220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 25 time to evaluate : 0.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 8 optimal weight: 10.0000 chunk 11 optimal weight: 10.0000 chunk 19 optimal weight: 8.9990 chunk 17 optimal weight: 7.9990 chunk 12 optimal weight: 4.9990 chunk 10 optimal weight: 10.0000 chunk 7 optimal weight: 1.9990 chunk 5 optimal weight: 10.0000 chunk 4 optimal weight: 2.9990 chunk 18 optimal weight: 8.9990 chunk 6 optimal weight: 3.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.101491 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.077990 restraints weight = 20355.324| |-----------------------------------------------------------------------------| r_work (start): 0.3215 rms_B_bonded: 6.01 r_work: 0.3005 rms_B_bonded: 4.96 restraints_weight: 0.5000 r_work (final): 0.3005 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3058 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3058 r_free = 0.3058 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3058 r_free = 0.3058 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3058 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.2068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.025 2220 Z= 0.494 Angle : 0.611 7.301 3020 Z= 0.338 Chirality : 0.046 0.127 340 Planarity : 0.004 0.010 400 Dihedral : 4.451 9.522 310 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 0.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.31 % Favored : 92.69 % Rotamer: Outliers : 0.42 % Allowed : 5.00 % Favored : 94.58 % 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: -4.98 (0.25), residues: 270 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.79 (0.19), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.017 0.004 PHE G 15 TYR 0.005 0.001 TYR A 37 ARG 0.001 0.000 ARG B 11 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 540 Ramachandran restraints generated. 270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 540 Ramachandran restraints generated. 270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 31 residues out of total 220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 30 time to evaluate : 0.234 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 31 average time/residue: 0.0628 time to fit residues: 2.8698 Evaluate side-chains 27 residues out of total 220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 26 time to evaluate : 0.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 28 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 12 optimal weight: 10.0000 chunk 10 optimal weight: 8.9990 chunk 1 optimal weight: 5.9990 chunk 4 optimal weight: 7.9990 chunk 11 optimal weight: 0.7980 chunk 17 optimal weight: 5.9990 chunk 15 optimal weight: 4.9990 chunk 16 optimal weight: 3.9990 chunk 9 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 5 optimal weight: 0.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 35 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.108787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.084508 restraints weight = 16572.914| |-----------------------------------------------------------------------------| r_work (start): 0.3279 rms_B_bonded: 5.64 r_work: 0.3060 rms_B_bonded: 4.95 restraints_weight: 0.5000 r_work (final): 0.3060 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3067 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3067 r_free = 0.3067 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3067 r_free = 0.3067 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3067 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.2296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.018 2220 Z= 0.227 Angle : 0.465 7.796 3020 Z= 0.251 Chirality : 0.043 0.126 340 Planarity : 0.002 0.005 400 Dihedral : 3.645 7.847 310 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 0.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.15 % Favored : 98.85 % Rotamer: Outliers : 1.67 % Allowed : 7.08 % Favored : 91.25 % 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: -4.98 (0.28), residues: 270 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.79 (0.21), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.010 0.002 PHE F 15 TYR 0.003 0.001 TYR G 37 ARG 0.000 0.000 ARG B 11 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 540 Ramachandran restraints generated. 270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 540 Ramachandran restraints generated. 270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 32 residues out of total 220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 28 time to evaluate : 0.231 Fit side-chains REVERT: G 19 SER cc_start: 0.8722 (t) cc_final: 0.8313 (p) REVERT: H 19 SER cc_start: 0.8561 (t) cc_final: 0.8221 (p) REVERT: I 11 ARG cc_start: 0.8005 (mtt180) cc_final: 0.7543 (mtm-85) outliers start: 4 outliers final: 4 residues processed: 30 average time/residue: 0.0960 time to fit residues: 3.7422 Evaluate side-chains 32 residues out of total 220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 28 time to evaluate : 0.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 SER Chi-restraints excluded: chain B residue 28 SER Chi-restraints excluded: chain G residue 28 SER Chi-restraints excluded: chain I residue 28 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 11 optimal weight: 7.9990 chunk 18 optimal weight: 10.0000 chunk 19 optimal weight: 0.6980 chunk 12 optimal weight: 10.0000 chunk 10 optimal weight: 10.0000 chunk 0 optimal weight: 8.9990 chunk 3 optimal weight: 6.9990 chunk 14 optimal weight: 0.9980 chunk 6 optimal weight: 1.9990 chunk 9 optimal weight: 4.9990 chunk 8 optimal weight: 1.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 35 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.108725 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.084755 restraints weight = 17112.325| |-----------------------------------------------------------------------------| r_work (start): 0.3288 rms_B_bonded: 5.39 r_work: 0.3063 rms_B_bonded: 5.02 restraints_weight: 2.0000 r_work (final): 0.3063 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3066 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3066 r_free = 0.3066 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3066 r_free = 0.3066 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3066 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.2433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.018 2220 Z= 0.246 Angle : 0.471 7.055 3020 Z= 0.255 Chirality : 0.043 0.124 340 Planarity : 0.002 0.005 400 Dihedral : 3.704 8.268 310 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 0.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.15 % Favored : 93.85 % Rotamer: Outliers : 2.08 % Allowed : 7.92 % Favored : 90.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.97 (0.29), residues: 270 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.78 (0.22), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.010 0.002 PHE H 15 TYR 0.007 0.001 TYR G 37 ARG 0.000 0.000 ARG D 11 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 540 Ramachandran restraints generated. 270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 540 Ramachandran restraints generated. 270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 30 time to evaluate : 0.209 Fit side-chains REVERT: G 19 SER cc_start: 0.8695 (t) cc_final: 0.8267 (p) REVERT: H 19 SER cc_start: 0.8616 (t) cc_final: 0.8220 (p) REVERT: I 11 ARG cc_start: 0.8024 (mtt180) cc_final: 0.7573 (mtm-85) outliers start: 5 outliers final: 5 residues processed: 31 average time/residue: 0.0903 time to fit residues: 3.6798 Evaluate side-chains 34 residues out of total 220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 29 time to evaluate : 0.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 SER Chi-restraints excluded: chain B residue 28 SER Chi-restraints excluded: chain F residue 28 SER Chi-restraints excluded: chain H residue 28 SER Chi-restraints excluded: chain I residue 28 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 16 optimal weight: 9.9990 chunk 9 optimal weight: 7.9990 chunk 11 optimal weight: 6.9990 chunk 7 optimal weight: 0.9990 chunk 8 optimal weight: 8.9990 chunk 0 optimal weight: 8.9990 chunk 10 optimal weight: 6.9990 chunk 3 optimal weight: 0.9980 chunk 19 optimal weight: 5.9990 chunk 17 optimal weight: 0.7980 chunk 5 optimal weight: 0.9980 overall best weight: 1.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.108662 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.084377 restraints weight = 17046.774| |-----------------------------------------------------------------------------| r_work (start): 0.3287 rms_B_bonded: 5.30 r_work: 0.3059 rms_B_bonded: 5.05 restraints_weight: 2.0000 r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3063 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3063 r_free = 0.3063 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3063 r_free = 0.3063 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3063 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.2510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.018 2220 Z= 0.224 Angle : 0.459 6.588 3020 Z= 0.249 Chirality : 0.043 0.124 340 Planarity : 0.002 0.005 400 Dihedral : 3.628 7.825 310 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 0.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 1.67 % Allowed : 9.58 % Favored : 88.75 % 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: -4.91 (0.30), residues: 270 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.73 (0.23), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.010 0.002 PHE H 15 TYR 0.008 0.001 TYR G 37 ARG 0.000 0.000 ARG E 11 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 540 Ramachandran restraints generated. 270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 540 Ramachandran restraints generated. 270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 32 time to evaluate : 0.241 Fit side-chains REVERT: G 19 SER cc_start: 0.8607 (t) cc_final: 0.8208 (p) REVERT: H 19 SER cc_start: 0.8575 (t) cc_final: 0.8193 (p) REVERT: I 11 ARG cc_start: 0.8003 (mtt180) cc_final: 0.7559 (mtm-85) outliers start: 4 outliers final: 4 residues processed: 32 average time/residue: 0.0925 time to fit residues: 3.9050 Evaluate side-chains 34 residues out of total 220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 30 time to evaluate : 0.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 28 SER Chi-restraints excluded: chain G residue 28 SER Chi-restraints excluded: chain H residue 28 SER Chi-restraints excluded: chain I residue 28 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 51.7781 > 50: distance: 3 - 105: 7.965 distance: 46 - 143: 4.267 distance: 90 - 99: 5.247 distance: 99 - 100: 5.354 distance: 99 - 188: 7.691 distance: 100 - 103: 3.459 distance: 101 - 102: 6.909 distance: 102 - 196: 12.281 distance: 103 - 104: 6.635 distance: 105 - 106: 11.459 distance: 106 - 107: 9.936 distance: 107 - 108: 10.148 distance: 107 - 109: 7.737 distance: 110 - 111: 10.612 distance: 110 - 113: 10.813 distance: 111 - 112: 4.451 distance: 113 - 114: 10.555 distance: 114 - 115: 5.543 distance: 114 - 116: 4.876 distance: 117 - 118: 9.664 distance: 118 - 119: 20.309 distance: 119 - 120: 17.116 distance: 119 - 125: 3.483 distance: 121 - 122: 12.735 distance: 122 - 123: 4.625 distance: 122 - 124: 3.555 distance: 125 - 126: 14.153 distance: 126 - 127: 10.970 distance: 126 - 129: 8.976 distance: 127 - 128: 15.330 distance: 127 - 136: 13.020 distance: 129 - 130: 6.615 distance: 130 - 131: 10.669 distance: 130 - 132: 13.603 distance: 131 - 133: 8.492 distance: 132 - 134: 6.674 distance: 133 - 135: 11.570 distance: 134 - 135: 15.644 distance: 137 - 138: 12.799 distance: 138 - 139: 11.590 distance: 138 - 140: 12.093 distance: 140 - 141: 13.117 distance: 141 - 142: 17.259 distance: 141 - 144: 13.475 distance: 142 - 143: 9.974 distance: 142 - 145: 10.123 distance: 145 - 146: 9.668 distance: 145 - 234: 14.169 distance: 146 - 147: 20.558 distance: 146 - 149: 6.690 distance: 147 - 148: 19.477 distance: 147 - 153: 42.656 distance: 149 - 150: 6.574 distance: 149 - 151: 31.864 distance: 150 - 152: 10.530 distance: 153 - 154: 7.049 distance: 154 - 155: 29.267 distance: 154 - 157: 17.335 distance: 155 - 156: 10.334 distance: 155 - 161: 5.773 distance: 157 - 158: 14.780 distance: 158 - 159: 17.214 distance: 158 - 160: 17.741 distance: 161 - 162: 16.543 distance: 162 - 163: 4.189 distance: 162 - 165: 12.058 distance: 163 - 164: 6.620 distance: 163 - 167: 4.935 distance: 165 - 166: 11.832