Starting phenix.real_space_refine on Mon Jun 24 17:26:03 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jvm_36677/06_2024/8jvm_36677.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jvm_36677/06_2024/8jvm_36677.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.86 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jvm_36677/06_2024/8jvm_36677.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jvm_36677/06_2024/8jvm_36677.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jvm_36677/06_2024/8jvm_36677.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jvm_36677/06_2024/8jvm_36677.pdb" } resolution = 3.86 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= -0.003 sd= 0.021 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 15 5.16 5 C 2310 2.51 5 N 636 2.21 5 O 765 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "F PHE 947": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 846": "OE1" <-> "OE2" Residue "J GLU 847": "OE1" <-> "OE2" Residue "J GLU 851": "OE1" <-> "OE2" Residue "J ASP 961": "OD1" <-> "OD2" Residue "Z PHE 929": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/chem_data/mon_lib" Total number of atoms: 3726 Number of models: 1 Model: "" Number of chains: 3 Chain: "F" Number of atoms: 1242 Number of conformers: 1 Conformer: "" Number of residues, atoms: 166, 1242 Classifications: {'peptide': 166} Link IDs: {'PTRANS': 6, 'TRANS': 159} Chain: "J" Number of atoms: 1242 Number of conformers: 1 Conformer: "" Number of residues, atoms: 166, 1242 Classifications: {'peptide': 166} Link IDs: {'PTRANS': 6, 'TRANS': 159} Chain: "Z" Number of atoms: 1242 Number of conformers: 1 Conformer: "" Number of residues, atoms: 166, 1242 Classifications: {'peptide': 166} Link IDs: {'PTRANS': 6, 'TRANS': 159} Time building chain proxies: 3.64, per 1000 atoms: 0.98 Number of scatterers: 3726 At special positions: 0 Unit cell: (63.3778, 65.5262, 157.907, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 15 16.00 O 765 8.00 N 636 7.00 C 2310 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 - 3.50 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: 1.44 Conformation dependent library (CDL) restraints added in 636.1 milliseconds 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 918 Finding SS restraints... Secondary structure from input PDB file: 5 helices and 10 sheets defined 23.5% alpha, 18.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.37 Creating SS restraints... Processing helix chain 'F' and resid 831 through 866 removed outlier: 3.637A pdb=" N VAL F 835 " --> pdb=" O LEU F 831 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N THR F 838 " --> pdb=" O LYS F 834 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N GLU F 839 " --> pdb=" O VAL F 835 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N ALA F 864 " --> pdb=" O ASN F 860 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N VAL F 865 " --> pdb=" O ALA F 861 " (cutoff:3.500A) Processing helix chain 'F' and resid 918 through 922 removed outlier: 4.178A pdb=" N ASN F 921 " --> pdb=" O ALA F 918 " (cutoff:3.500A) Processing helix chain 'J' and resid 831 through 866 removed outlier: 4.193A pdb=" N VAL J 835 " --> pdb=" O LEU J 831 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N GLU J 836 " --> pdb=" O LEU J 832 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ARG J 844 " --> pdb=" O ASP J 840 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLU J 846 " --> pdb=" O ALA J 842 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N GLU J 847 " --> pdb=" O SER J 843 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ALA J 864 " --> pdb=" O ASN J 860 " (cutoff:3.500A) Processing helix chain 'J' and resid 907 through 911 Processing helix chain 'Z' and resid 832 through 866 removed outlier: 3.534A pdb=" N THR Z 838 " --> pdb=" O LYS Z 834 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N GLU Z 839 " --> pdb=" O VAL Z 835 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ALA Z 864 " --> pdb=" O ASN Z 860 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N VAL Z 865 " --> pdb=" O ALA Z 861 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'F' and resid 882 through 887 Processing sheet with id=AA2, first strand: chain 'F' and resid 932 through 934 removed outlier: 6.689A pdb=" N LEU F 933 " --> pdb=" O THR Z 939 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'F' and resid 955 through 957 removed outlier: 6.486A pdb=" N LEU F 955 " --> pdb=" O ASP Z 961 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'F' and resid 959 through 962 removed outlier: 5.775A pdb=" N ASN F 959 " --> pdb=" O LEU J 955 " (cutoff:3.500A) removed outlier: 7.067A pdb=" N ALA J 957 " --> pdb=" O ASN F 959 " (cutoff:3.500A) removed outlier: 5.731A pdb=" N ASP F 961 " --> pdb=" O ALA J 957 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'F' and resid 988 through 989 removed outlier: 3.647A pdb=" N ILE Z 978 " --> pdb=" O THR J 983 " (cutoff:3.500A) removed outlier: 7.163A pdb=" N LEU Z 973 " --> pdb=" O ASN F 967 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N ASN F 969 " --> pdb=" O LEU Z 973 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N ASN J 967 " --> pdb=" O GLY F 971 " (cutoff:3.500A) removed outlier: 7.401A pdb=" N LEU F 973 " --> pdb=" O ASN J 967 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N ASN J 969 " --> pdb=" O LEU F 973 " (cutoff:3.500A) removed outlier: 7.865A pdb=" N ALA Z 968 " --> pdb=" O SER J 970 " (cutoff:3.500A) removed outlier: 5.995A pdb=" N THR J 972 " --> pdb=" O ALA Z 968 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'J' and resid 960 through 962 removed outlier: 6.341A pdb=" N ASN F 967 " --> pdb=" O ILE J 962 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N THR Z 983 " --> pdb=" O SER F 974 " (cutoff:3.500A) removed outlier: 5.778A pdb=" N VAL F 976 " --> pdb=" O THR Z 983 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'J' and resid 976 through 978 removed outlier: 5.538A pdb=" N THR F 983 " --> pdb=" O ILE J 978 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'J' and resid 881 through 886 Processing sheet with id=AA9, first strand: chain 'J' and resid 905 through 906 removed outlier: 4.156A pdb=" N THR J 913 " --> pdb=" O ASP J 906 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'Z' and resid 881 through 884 removed outlier: 3.615A pdb=" N GLY Z 881 " --> pdb=" O LEU Z 896 " (cutoff:3.500A) 112 hydrogen bonds defined for protein. 318 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: 0.87 Time building geometry restraints manager: 1.59 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 692 1.32 - 1.44: 859 1.44 - 1.57: 2195 1.57 - 1.69: 4 1.69 - 1.81: 27 Bond restraints: 3777 Sorted by residual: bond pdb=" N PRO Z 945 " pdb=" CA PRO Z 945 " ideal model delta sigma weight residual 1.469 1.579 -0.110 1.28e-02 6.10e+03 7.39e+01 bond pdb=" N ALA Z 946 " pdb=" CA ALA Z 946 " ideal model delta sigma weight residual 1.457 1.529 -0.072 1.29e-02 6.01e+03 3.10e+01 bond pdb=" CA PRO Z 944 " pdb=" C PRO Z 944 " ideal model delta sigma weight residual 1.517 1.566 -0.049 9.30e-03 1.16e+04 2.73e+01 bond pdb=" C PRO Z 945 " pdb=" N ALA Z 946 " ideal model delta sigma weight residual 1.332 1.394 -0.061 1.40e-02 5.10e+03 1.91e+01 bond pdb=" C PRO Z 944 " pdb=" O PRO Z 944 " ideal model delta sigma weight residual 1.240 1.193 0.048 1.12e-02 7.97e+03 1.82e+01 ... (remaining 3772 not shown) Histogram of bond angle deviations from ideal: 98.41 - 105.56: 74 105.56 - 112.70: 1992 112.70 - 119.85: 1274 119.85 - 127.00: 1737 127.00 - 134.14: 35 Bond angle restraints: 5112 Sorted by residual: angle pdb=" C PRO Z 944 " pdb=" CA PRO Z 944 " pdb=" CB PRO Z 944 " ideal model delta sigma weight residual 110.92 128.26 -17.34 1.22e+00 6.72e-01 2.02e+02 angle pdb=" N PRO Z 945 " pdb=" CA PRO Z 945 " pdb=" C PRO Z 945 " ideal model delta sigma weight residual 112.47 132.37 -19.90 2.06e+00 2.36e-01 9.33e+01 angle pdb=" CA ASN Z 943 " pdb=" C ASN Z 943 " pdb=" N PRO Z 944 " ideal model delta sigma weight residual 117.69 125.70 -8.01 9.30e-01 1.16e+00 7.43e+01 angle pdb=" C PRO Z 944 " pdb=" N PRO Z 945 " pdb=" CA PRO Z 945 " ideal model delta sigma weight residual 119.84 129.01 -9.17 1.25e+00 6.40e-01 5.39e+01 angle pdb=" N ALA Z 946 " pdb=" CA ALA Z 946 " pdb=" C ALA Z 946 " ideal model delta sigma weight residual 110.80 125.60 -14.80 2.13e+00 2.20e-01 4.82e+01 ... (remaining 5107 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.81: 2070 17.81 - 35.62: 185 35.62 - 53.43: 43 53.43 - 71.24: 3 71.24 - 89.05: 3 Dihedral angle restraints: 2304 sinusoidal: 888 harmonic: 1416 Sorted by residual: dihedral pdb=" C PRO Z 944 " pdb=" N PRO Z 944 " pdb=" CA PRO Z 944 " pdb=" CB PRO Z 944 " ideal model delta harmonic sigma weight residual -120.70 -133.09 12.39 0 2.50e+00 1.60e-01 2.46e+01 dihedral pdb=" CA ALA Z 899 " pdb=" C ALA Z 899 " pdb=" N ASN Z 900 " pdb=" CA ASN Z 900 " ideal model delta harmonic sigma weight residual -180.00 -156.77 -23.23 0 5.00e+00 4.00e-02 2.16e+01 dihedral pdb=" CA PRO F 907 " pdb=" C PRO F 907 " pdb=" N ALA F 908 " pdb=" CA ALA F 908 " ideal model delta harmonic sigma weight residual 180.00 158.56 21.44 0 5.00e+00 4.00e-02 1.84e+01 ... (remaining 2301 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.065: 478 0.065 - 0.130: 92 0.130 - 0.194: 17 0.194 - 0.259: 2 0.259 - 0.323: 2 Chirality restraints: 591 Sorted by residual: chirality pdb=" CA ALA Z 946 " pdb=" N ALA Z 946 " pdb=" C ALA Z 946 " pdb=" CB ALA Z 946 " both_signs ideal model delta sigma weight residual False 2.48 2.16 0.32 2.00e-01 2.50e+01 2.62e+00 chirality pdb=" CA PRO Z 944 " pdb=" N PRO Z 944 " pdb=" C PRO Z 944 " pdb=" CB PRO Z 944 " both_signs ideal model delta sigma weight residual False 2.72 2.43 0.29 2.00e-01 2.50e+01 2.15e+00 chirality pdb=" CA GLU J 836 " pdb=" N GLU J 836 " pdb=" C GLU J 836 " pdb=" CB GLU J 836 " both_signs ideal model delta sigma weight residual False 2.51 2.74 -0.23 2.00e-01 2.50e+01 1.30e+00 ... (remaining 588 not shown) Planarity restraints: 678 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU J 832 " 0.023 2.00e-02 2.50e+03 4.61e-02 2.13e+01 pdb=" C LEU J 832 " -0.080 2.00e-02 2.50e+03 pdb=" O LEU J 832 " 0.030 2.00e-02 2.50e+03 pdb=" N GLU J 833 " 0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP Z 859 " -0.023 2.00e-02 2.50e+03 2.51e-02 1.57e+01 pdb=" CG TRP Z 859 " 0.068 2.00e-02 2.50e+03 pdb=" CD1 TRP Z 859 " -0.032 2.00e-02 2.50e+03 pdb=" CD2 TRP Z 859 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP Z 859 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP Z 859 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP Z 859 " -0.009 2.00e-02 2.50e+03 pdb=" CZ2 TRP Z 859 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP Z 859 " -0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP Z 859 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN Z 943 " 0.016 2.00e-02 2.50e+03 3.22e-02 1.03e+01 pdb=" C ASN Z 943 " -0.056 2.00e-02 2.50e+03 pdb=" O ASN Z 943 " 0.019 2.00e-02 2.50e+03 pdb=" N PRO Z 944 " 0.020 2.00e-02 2.50e+03 ... (remaining 675 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 156 2.69 - 3.24: 3970 3.24 - 3.80: 6002 3.80 - 4.35: 7491 4.35 - 4.90: 11942 Nonbonded interactions: 29561 Sorted by model distance: nonbonded pdb=" O ASN Z 943 " pdb=" C PRO Z 944 " model vdw 2.138 3.270 nonbonded pdb=" O PRO F 907 " pdb=" NH1 ARG J 901 " model vdw 2.160 2.520 nonbonded pdb=" O ALA J 946 " pdb=" OG1 THR J 956 " model vdw 2.169 2.440 nonbonded pdb=" O GLY Z 986 " pdb=" OG1 THR Z 987 " model vdw 2.196 2.440 nonbonded pdb=" OG SER F 883 " pdb=" OE2 GLU F 885 " model vdw 2.203 2.440 ... (remaining 29556 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'F' selection = chain 'J' selection = chain 'Z' } 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: 3.760 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: 12.940 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 15.760 Find NCS groups from input model: 0.220 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:2.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5528 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 0.110 3777 Z= 0.357 Angle : 1.085 19.900 5112 Z= 0.673 Chirality : 0.056 0.323 591 Planarity : 0.006 0.052 678 Dihedral : 14.544 89.053 1386 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 27.03 Ramachandran Plot: Outliers : 1.63 % Allowed : 16.26 % Favored : 82.11 % Rotamer: Outliers : 1.75 % Allowed : 1.75 % Favored : 96.49 % Cbeta Deviations : 0.22 % 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: -3.56 (0.34), residues: 492 helix: 0.67 (0.53), residues: 98 sheet: -2.56 (0.70), residues: 48 loop : -3.57 (0.28), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.068 0.003 TRP Z 859 HIS 0.001 0.000 HIS F 875 PHE 0.022 0.002 PHE Z 848 TYR 0.010 0.002 TYR Z 876 ARG 0.008 0.001 ARG J 901 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 399 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 85 time to evaluate : 0.391 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Z 976 VAL cc_start: 0.5104 (t) cc_final: 0.4797 (t) outliers start: 7 outliers final: 3 residues processed: 90 average time/residue: 0.1758 time to fit residues: 18.8437 Evaluate side-chains 69 residues out of total 399 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 66 time to evaluate : 0.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 840 ASP Chi-restraints excluded: chain Z residue 943 ASN Chi-restraints excluded: chain Z residue 944 PRO Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 40 optimal weight: 0.3980 chunk 36 optimal weight: 0.9980 chunk 20 optimal weight: 3.9990 chunk 12 optimal weight: 5.9990 chunk 24 optimal weight: 0.9980 chunk 19 optimal weight: 0.7980 chunk 37 optimal weight: 1.9990 chunk 14 optimal weight: 0.7980 chunk 22 optimal weight: 0.2980 chunk 28 optimal weight: 0.4980 chunk 43 optimal weight: 0.4980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 959 ASN ** J 875 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 959 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5513 moved from start: 0.1421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 3777 Z= 0.208 Angle : 0.716 7.134 5112 Z= 0.381 Chirality : 0.044 0.221 591 Planarity : 0.006 0.084 678 Dihedral : 7.267 53.219 517 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 22.44 Ramachandran Plot: Outliers : 0.61 % Allowed : 14.23 % Favored : 85.16 % Rotamer: Outliers : 3.26 % Allowed : 13.78 % Favored : 82.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.56 % 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: -3.19 (0.35), residues: 492 helix: 1.40 (0.51), residues: 96 sheet: -2.57 (0.70), residues: 44 loop : -3.39 (0.28), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP Z 859 HIS 0.011 0.003 HIS J 875 PHE 0.019 0.002 PHE Z 848 TYR 0.007 0.002 TYR Z 876 ARG 0.004 0.000 ARG J 901 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 399 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 69 time to evaluate : 0.421 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 862 MET cc_start: 0.6848 (mpp) cc_final: 0.6266 (mpp) REVERT: Z 832 LEU cc_start: 0.7051 (OUTLIER) cc_final: 0.6762 (pp) outliers start: 13 outliers final: 8 residues processed: 76 average time/residue: 0.2011 time to fit residues: 18.0643 Evaluate side-chains 73 residues out of total 399 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 64 time to evaluate : 0.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 952 ASP Chi-restraints excluded: chain F residue 963 SER Chi-restraints excluded: chain J residue 840 ASP Chi-restraints excluded: chain J residue 854 ASP Chi-restraints excluded: chain Z residue 832 LEU Chi-restraints excluded: chain Z residue 865 VAL Chi-restraints excluded: chain Z residue 924 PHE Chi-restraints excluded: chain Z residue 943 ASN Chi-restraints excluded: chain Z residue 944 PRO Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 24 optimal weight: 5.9990 chunk 13 optimal weight: 3.9990 chunk 36 optimal weight: 0.0670 chunk 29 optimal weight: 0.8980 chunk 12 optimal weight: 4.9990 chunk 43 optimal weight: 0.5980 chunk 47 optimal weight: 0.0570 chunk 38 optimal weight: 0.2980 chunk 14 optimal weight: 0.8980 chunk 35 optimal weight: 0.9990 chunk 32 optimal weight: 0.4980 overall best weight: 0.3036 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 959 ASN J 875 HIS Z 900 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5441 moved from start: 0.1923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 3777 Z= 0.175 Angle : 0.682 6.950 5112 Z= 0.356 Chirality : 0.044 0.233 591 Planarity : 0.006 0.098 678 Dihedral : 6.745 49.642 517 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 20.55 Ramachandran Plot: Outliers : 0.61 % Allowed : 14.43 % Favored : 84.96 % Rotamer: Outliers : 2.76 % Allowed : 18.80 % Favored : 78.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.56 % 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: -2.98 (0.35), residues: 492 helix: 1.67 (0.48), residues: 94 sheet: -2.54 (0.68), residues: 44 loop : -3.23 (0.29), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP Z 859 HIS 0.009 0.002 HIS J 875 PHE 0.014 0.002 PHE Z 848 TYR 0.022 0.003 TYR Z 876 ARG 0.005 0.001 ARG F 932 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 399 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 73 time to evaluate : 0.412 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 915 MET cc_start: 0.6524 (ppp) cc_final: 0.6027 (ptp) REVERT: Z 832 LEU cc_start: 0.6963 (mp) cc_final: 0.6662 (pp) outliers start: 11 outliers final: 6 residues processed: 80 average time/residue: 0.2044 time to fit residues: 19.2925 Evaluate side-chains 71 residues out of total 399 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 65 time to evaluate : 0.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 952 ASP Chi-restraints excluded: chain J residue 840 ASP Chi-restraints excluded: chain J residue 854 ASP Chi-restraints excluded: chain Z residue 865 VAL Chi-restraints excluded: chain Z residue 943 ASN Chi-restraints excluded: chain Z residue 944 PRO Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/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-5370/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/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-5370/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 700, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 764, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/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-5370/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-5370/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-5370/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-5370/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-5370/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-5370/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/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-5370/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-5370/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1477, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1379, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1260, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 65.1727 > 50: distance: 20 - 27: 10.680 distance: 27 - 28: 5.924 distance: 28 - 29: 15.361 distance: 28 - 31: 11.944 distance: 29 - 30: 24.524 distance: 29 - 36: 14.344 distance: 31 - 32: 14.512 distance: 32 - 33: 13.217 distance: 33 - 34: 10.045 distance: 33 - 35: 11.913 distance: 36 - 37: 14.695 distance: 37 - 38: 7.595 distance: 37 - 40: 12.353 distance: 38 - 39: 17.032 distance: 38 - 43: 9.801 distance: 40 - 41: 15.120 distance: 40 - 42: 7.005 distance: 43 - 44: 15.105 distance: 44 - 45: 8.437 distance: 44 - 47: 18.916 distance: 45 - 46: 21.186 distance: 45 - 52: 22.017 distance: 47 - 48: 21.380 distance: 48 - 49: 15.829 distance: 49 - 50: 9.132 distance: 50 - 51: 9.723 distance: 52 - 53: 9.546 distance: 53 - 54: 6.122 distance: 53 - 56: 17.872 distance: 54 - 55: 31.889 distance: 54 - 60: 9.711 distance: 56 - 57: 13.399 distance: 57 - 58: 7.536 distance: 57 - 59: 14.561 distance: 60 - 61: 31.020 distance: 61 - 62: 23.663 distance: 62 - 63: 52.359 distance: 62 - 64: 16.879 distance: 64 - 65: 16.965 distance: 65 - 66: 8.441 distance: 65 - 68: 18.656 distance: 66 - 67: 12.346 distance: 66 - 73: 15.025 distance: 68 - 69: 23.671 distance: 69 - 70: 15.406 distance: 70 - 71: 27.747 distance: 71 - 72: 17.122 distance: 73 - 74: 18.263 distance: 74 - 75: 14.501 distance: 75 - 76: 20.682 distance: 75 - 83: 11.932 distance: 77 - 78: 15.144 distance: 78 - 80: 5.698 distance: 79 - 81: 6.108 distance: 81 - 82: 5.166 distance: 83 - 84: 19.629 distance: 84 - 85: 21.292 distance: 84 - 87: 14.103 distance: 85 - 86: 23.033 distance: 85 - 95: 20.198 distance: 87 - 88: 7.659 distance: 88 - 89: 6.623 distance: 88 - 90: 16.129 distance: 89 - 91: 10.884 distance: 90 - 92: 7.708 distance: 91 - 93: 8.673 distance: 92 - 93: 8.937 distance: 93 - 94: 5.962 distance: 95 - 96: 5.018 distance: 96 - 97: 8.271 distance: 96 - 99: 7.839 distance: 97 - 98: 10.591 distance: 97 - 102: 19.029 distance: 99 - 100: 16.606 distance: 99 - 101: 18.254 distance: 102 - 103: 4.116 distance: 103 - 104: 7.314 distance: 103 - 106: 10.884 distance: 104 - 105: 16.296 distance: 104 - 107: 9.843