Starting phenix.real_space_refine on Wed Nov 15 18:52:13 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8peo_17633/11_2023/8peo_17633_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8peo_17633/11_2023/8peo_17633.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.69 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8peo_17633/11_2023/8peo_17633.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8peo_17633/11_2023/8peo_17633.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8peo_17633/11_2023/8peo_17633_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8peo_17633/11_2023/8peo_17633_updated.pdb" } resolution = 2.69 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= 0.013 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 294 5.49 5 S 13 5.16 5 C 7171 2.51 5 N 2399 2.21 5 O 2958 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 50": "OE1" <-> "OE2" Residue "A GLU 97": "OE1" <-> "OE2" Residue "B GLU 63": "OE1" <-> "OE2" Residue "C GLU 41": "OE1" <-> "OE2" Residue "C GLU 91": "OE1" <-> "OE2" Residue "D GLU 32": "OE1" <-> "OE2" Residue "D GLU 68": "OE1" <-> "OE2" Residue "D GLU 73": "OE1" <-> "OE2" Residue "D GLU 110": "OE1" <-> "OE2" Residue "E GLU 50": "OE1" <-> "OE2" Residue "F GLU 63": "OE1" <-> "OE2" Residue "F GLU 74": "OE1" <-> "OE2" Residue "G GLU 41": "OE1" <-> "OE2" Residue "G GLU 56": "OE1" <-> "OE2" Residue "G GLU 61": "OE1" <-> "OE2" Residue "G GLU 64": "OE1" <-> "OE2" Residue "H GLU 73": "OE1" <-> "OE2" Residue "H GLU 90": "OE1" <-> "OE2" Residue "H GLU 102": "OE1" <-> "OE2" Residue "H GLU 110": "OE1" <-> "OE2" Residue "K GLU 83": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/chem_data/mon_lib" Total number of atoms: 12835 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 817 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 4, 'TRANS': 94} Chain breaks: 1 Chain: "B" Number of atoms: 657 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 657 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 1, 'TRANS': 80} Chain: "C" Number of atoms: 823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 823 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Chain: "D" Number of atoms: 736 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 736 Classifications: {'peptide': 94} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 91} Chain: "E" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 801 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 3, 'TRANS': 93} Chain: "F" Number of atoms: 694 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 694 Classifications: {'peptide': 86} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 84} Chain: "G" Number of atoms: 823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 823 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Chain: "H" Number of atoms: 736 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 736 Classifications: {'peptide': 94} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 91} Chain: "I" Number of atoms: 2996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 2996 Classifications: {'DNA': 147} Link IDs: {'rna3p': 146} Chain: "K" Number of atoms: 710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 710 Classifications: {'peptide': 86} Link IDs: {'PTRANS': 11, 'TRANS': 74} Chain breaks: 1 Chain: "J" Number of atoms: 3031 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 3031 Classifications: {'DNA': 147} Link IDs: {'rna3p': 146} Chain: "A" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 11 Classifications: {'peptide': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'M2L:plan-1': 1} Unresolved non-hydrogen planarities: 1 Time building chain proxies: 7.15, per 1000 atoms: 0.56 Number of scatterers: 12835 At special positions: 0 Unit cell: (91.696, 119.205, 138.378, 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 13 16.00 P 294 15.00 O 2958 8.00 N 2399 7.00 C 7171 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 7.01 Conformation dependent library (CDL) restraints added in 1.3 seconds 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1598 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 36 helices and 1 sheets defined 57.7% alpha, 2.0% beta 146 base pairs and 270 stacking pairs defined. Time for finding SS restraints: 7.65 Creating SS restraints... Processing helix chain 'A' and resid 45 through 54 Processing helix chain 'A' and resid 64 through 76 removed outlier: 3.937A pdb=" N GLN A 76 " --> pdb=" O ARG A 72 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 113 Processing helix chain 'A' and resid 121 through 131 Processing helix chain 'B' and resid 26 through 28 No H-bonds generated for 'chain 'B' and resid 26 through 28' Processing helix chain 'B' and resid 31 through 41 Processing helix chain 'B' and resid 50 through 75 removed outlier: 3.725A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 83 through 93 removed outlier: 3.569A pdb=" N GLN B 93 " --> pdb=" O ALA B 89 " (cutoff:3.500A) Processing helix chain 'C' and resid 17 through 21 Processing helix chain 'C' and resid 27 through 37 Processing helix chain 'C' and resid 47 through 72 Processing helix chain 'C' and resid 80 through 89 Processing helix chain 'C' and resid 91 through 96 Processing helix chain 'D' and resid 35 through 45 Processing helix chain 'D' and resid 53 through 81 Processing helix chain 'D' and resid 88 through 98 Processing helix chain 'D' and resid 101 through 120 removed outlier: 4.359A pdb=" N VAL D 108 " --> pdb=" O LYS D 105 " (cutoff:3.500A) Processing helix chain 'E' and resid 45 through 54 Processing helix chain 'E' and resid 64 through 77 removed outlier: 4.436A pdb=" N ASP E 77 " --> pdb=" O GLU E 73 " (cutoff:3.500A) Processing helix chain 'E' and resid 86 through 113 Processing helix chain 'E' and resid 121 through 131 Processing helix chain 'F' and resid 26 through 28 No H-bonds generated for 'chain 'F' and resid 26 through 28' Processing helix chain 'F' and resid 31 through 41 Processing helix chain 'F' and resid 48 through 75 removed outlier: 4.109A pdb=" N TYR F 51 " --> pdb=" O GLY F 48 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N GLU F 52 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ILE F 66 " --> pdb=" O GLU F 63 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ARG F 67 " --> pdb=" O ASN F 64 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ASP F 68 " --> pdb=" O VAL F 65 " (cutoff:3.500A) Processing helix chain 'F' and resid 83 through 92 Processing helix chain 'G' and resid 17 through 21 Processing helix chain 'G' and resid 27 through 36 Processing helix chain 'G' and resid 45 through 72 removed outlier: 4.397A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 80 through 88 Processing helix chain 'G' and resid 93 through 96 No H-bonds generated for 'chain 'G' and resid 93 through 96' Processing helix chain 'G' and resid 113 through 115 No H-bonds generated for 'chain 'G' and resid 113 through 115' Processing helix chain 'H' and resid 35 through 45 Processing helix chain 'H' and resid 53 through 80 Processing helix chain 'H' and resid 88 through 98 Processing helix chain 'H' and resid 101 through 120 removed outlier: 4.112A pdb=" N LYS H 105 " --> pdb=" O GLY H 101 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N HIS H 106 " --> pdb=" O GLU H 102 " (cutoff:3.500A) Processing helix chain 'K' and resid 77 through 82 Processing sheet with id= A, first strand: chain 'K' and resid 58 through 60 removed outlier: 3.839A pdb=" N GLU K 49 " --> pdb=" O PHE K 44 " (cutoff:3.500A) 353 hydrogen bonds defined for protein. 945 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 374 hydrogen bonds 748 hydrogen bond angles 0 basepair planarities 146 basepair parallelities 270 stacking parallelities Total time for adding SS restraints: 4.73 Time building geometry restraints manager: 7.41 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2228 1.33 - 1.45: 4599 1.45 - 1.57: 6234 1.57 - 1.69: 586 1.69 - 1.82: 26 Bond restraints: 13673 Sorted by residual: bond pdb=" N ARG E 129 " pdb=" CA ARG E 129 " ideal model delta sigma weight residual 1.459 1.488 -0.028 1.20e-02 6.94e+03 5.59e+00 bond pdb=" N ASP E 123 " pdb=" CA ASP E 123 " ideal model delta sigma weight residual 1.459 1.487 -0.028 1.20e-02 6.94e+03 5.49e+00 bond pdb=" C TRP K 21 " pdb=" N PRO K 22 " ideal model delta sigma weight residual 1.332 1.358 -0.026 1.12e-02 7.97e+03 5.43e+00 bond pdb=" N ARG B 36 " pdb=" CA ARG B 36 " ideal model delta sigma weight residual 1.459 1.486 -0.027 1.20e-02 6.94e+03 5.09e+00 bond pdb=" P DG I -49 " pdb=" OP1 DG I -49 " ideal model delta sigma weight residual 1.480 1.521 -0.041 2.00e-02 2.50e+03 4.22e+00 ... (remaining 13668 not shown) Histogram of bond angle deviations from ideal: 98.08 - 105.26: 1321 105.26 - 112.43: 7523 112.43 - 119.60: 4514 119.60 - 126.77: 5533 126.77 - 133.94: 830 Bond angle restraints: 19721 Sorted by residual: angle pdb=" C ILE B 34 " pdb=" N ARG B 35 " pdb=" CA ARG B 35 " ideal model delta sigma weight residual 120.29 114.32 5.97 1.42e+00 4.96e-01 1.77e+01 angle pdb=" CA ASN G 73 " pdb=" CB ASN G 73 " pdb=" CG ASN G 73 " ideal model delta sigma weight residual 112.60 116.80 -4.20 1.00e+00 1.00e+00 1.77e+01 angle pdb=" CA ASN C 73 " pdb=" CB ASN C 73 " pdb=" CG ASN C 73 " ideal model delta sigma weight residual 112.60 116.63 -4.03 1.00e+00 1.00e+00 1.62e+01 angle pdb=" CA GLU D 68 " pdb=" CB GLU D 68 " pdb=" CG GLU D 68 " ideal model delta sigma weight residual 114.10 121.58 -7.48 2.00e+00 2.50e-01 1.40e+01 angle pdb=" C ASN G 73 " pdb=" CA ASN G 73 " pdb=" CB ASN G 73 " ideal model delta sigma weight residual 110.56 116.29 -5.73 1.69e+00 3.50e-01 1.15e+01 ... (remaining 19716 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.44: 5550 35.44 - 70.87: 1621 70.87 - 106.31: 37 106.31 - 141.74: 3 141.74 - 177.18: 4 Dihedral angle restraints: 7215 sinusoidal: 4743 harmonic: 2472 Sorted by residual: dihedral pdb=" CD M2L A 201 " pdb=" CE M2L A 201 " pdb=" NZ M2L A 201 " pdb=" CM1 M2L A 201 " ideal model delta sinusoidal sigma weight residual 66.23 -97.71 163.94 1 3.00e+01 1.11e-03 2.09e+01 dihedral pdb=" C4' DT J 69 " pdb=" C3' DT J 69 " pdb=" O3' DT J 69 " pdb=" P DC J 70 " ideal model delta sinusoidal sigma weight residual 220.00 42.82 177.18 1 3.50e+01 8.16e-04 1.57e+01 dihedral pdb=" C4' DC J 68 " pdb=" C3' DC J 68 " pdb=" O3' DC J 68 " pdb=" P DT J 69 " ideal model delta sinusoidal sigma weight residual -140.00 24.39 -164.39 1 3.50e+01 8.16e-04 1.54e+01 ... (remaining 7212 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.104: 2154 0.104 - 0.208: 70 0.208 - 0.313: 1 0.313 - 0.417: 0 0.417 - 0.521: 4 Chirality restraints: 2229 Sorted by residual: chirality pdb=" P DG J 50 " pdb=" OP1 DG J 50 " pdb=" OP2 DG J 50 " pdb=" O5' DG J 50 " both_signs ideal model delta sigma weight residual True 2.35 -2.87 -0.52 2.00e-01 2.50e+01 6.78e+00 chirality pdb=" P DC J 49 " pdb=" OP1 DC J 49 " pdb=" OP2 DC J 49 " pdb=" O5' DC J 49 " both_signs ideal model delta sigma weight residual True 2.35 -2.86 -0.52 2.00e-01 2.50e+01 6.67e+00 chirality pdb=" P DC I -50 " pdb=" OP1 DC I -50 " pdb=" OP2 DC I -50 " pdb=" O5' DC I -50 " both_signs ideal model delta sigma weight residual True 2.35 -2.86 -0.52 2.00e-01 2.50e+01 6.65e+00 ... (remaining 2226 not shown) Planarity restraints: 1477 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN G 73 " -0.019 2.00e-02 2.50e+03 3.88e-02 1.51e+01 pdb=" C ASN G 73 " 0.067 2.00e-02 2.50e+03 pdb=" O ASN G 73 " -0.025 2.00e-02 2.50e+03 pdb=" N LYS G 74 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DC I 69 " -0.040 2.00e-02 2.50e+03 2.41e-02 1.31e+01 pdb=" N1 DC I 69 " 0.057 2.00e-02 2.50e+03 pdb=" C2 DC I 69 " -0.013 2.00e-02 2.50e+03 pdb=" O2 DC I 69 " 0.009 2.00e-02 2.50e+03 pdb=" N3 DC I 69 " -0.001 2.00e-02 2.50e+03 pdb=" C4 DC I 69 " -0.004 2.00e-02 2.50e+03 pdb=" N4 DC I 69 " -0.010 2.00e-02 2.50e+03 pdb=" C5 DC I 69 " -0.000 2.00e-02 2.50e+03 pdb=" C6 DC I 69 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DC I 49 " 0.030 2.00e-02 2.50e+03 2.39e-02 1.28e+01 pdb=" N1 DC I 49 " -0.057 2.00e-02 2.50e+03 pdb=" C2 DC I 49 " 0.028 2.00e-02 2.50e+03 pdb=" O2 DC I 49 " -0.010 2.00e-02 2.50e+03 pdb=" N3 DC I 49 " -0.003 2.00e-02 2.50e+03 pdb=" C4 DC I 49 " 0.003 2.00e-02 2.50e+03 pdb=" N4 DC I 49 " 0.003 2.00e-02 2.50e+03 pdb=" C5 DC I 49 " 0.006 2.00e-02 2.50e+03 pdb=" C6 DC I 49 " -0.001 2.00e-02 2.50e+03 ... (remaining 1474 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1281 2.74 - 3.28: 10780 3.28 - 3.82: 25225 3.82 - 4.36: 30151 4.36 - 4.90: 43125 Nonbonded interactions: 110562 Sorted by model distance: nonbonded pdb=" O GLU K 66 " pdb=" NZ LYS K 70 " model vdw 2.201 2.520 nonbonded pdb=" N GLU A 59 " pdb=" OE1 GLU A 59 " model vdw 2.204 2.520 nonbonded pdb=" NZ LYS H 43 " pdb=" O THR H 49 " model vdw 2.219 2.520 nonbonded pdb=" O TRP K 82 " pdb=" ND2 ASN K 86 " model vdw 2.241 2.520 nonbonded pdb=" OG1 THR F 73 " pdb=" OD2 ASP F 85 " model vdw 2.254 2.440 ... (remaining 110557 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 'A' and resid 38 through 134) selection = chain 'E' } ncs_group { reference = chain 'B' selection = (chain 'F' and resid 20 through 101) } ncs_group { reference = chain 'C' selection = chain 'G' } ncs_group { reference = chain 'D' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.040 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: 15.110 Check model and map are aligned: 0.200 Set scattering table: 0.120 Process input model: 43.770 Find NCS groups from input model: 0.490 Set up NCS constraints: 0.060 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: 0.010 Load rotamer database and sin/cos tables:12.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 77.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8565 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 : 0.005 0.048 13673 Z= 0.296 Angle : 0.772 8.793 19721 Z= 0.458 Chirality : 0.051 0.521 2229 Planarity : 0.006 0.119 1477 Dihedral : 29.931 177.176 5617 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 0.14 % Allowed : 20.20 % Favored : 79.66 % 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: 0.99 (0.29), residues: 831 helix: 1.68 (0.22), residues: 548 sheet: -2.59 (0.96), residues: 23 loop : -1.27 (0.34), residues: 260 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 713 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 166 time to evaluate : 1.024 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 167 average time/residue: 1.9065 time to fit residues: 336.4084 Evaluate side-chains 113 residues out of total 713 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 113 time to evaluate : 1.005 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.1820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 91 optimal weight: 5.9990 chunk 81 optimal weight: 4.9990 chunk 45 optimal weight: 8.9990 chunk 27 optimal weight: 0.8980 chunk 55 optimal weight: 3.9990 chunk 43 optimal weight: 0.7980 chunk 84 optimal weight: 2.9990 chunk 32 optimal weight: 0.1980 chunk 51 optimal weight: 0.3980 chunk 63 optimal weight: 0.9990 chunk 98 optimal weight: 4.9990 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 46 HIS H 92 GLN K 20 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8606 moved from start: 0.1927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 13673 Z= 0.202 Angle : 0.586 9.692 19721 Z= 0.350 Chirality : 0.035 0.135 2229 Planarity : 0.005 0.040 1477 Dihedral : 31.693 178.545 3903 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 2.24 % Allowed : 21.60 % Favored : 76.16 % 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: 1.52 (0.29), residues: 831 helix: 1.97 (0.22), residues: 555 sheet: -1.64 (1.16), residues: 21 loop : -0.91 (0.35), residues: 255 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 713 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 125 time to evaluate : 0.958 Fit side-chains revert: symmetry clash outliers start: 16 outliers final: 5 residues processed: 131 average time/residue: 1.7381 time to fit residues: 242.0610 Evaluate side-chains 122 residues out of total 713 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 117 time to evaluate : 0.948 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1473 time to fit residues: 2.3642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 54 optimal weight: 3.9990 chunk 30 optimal weight: 3.9990 chunk 81 optimal weight: 4.9990 chunk 66 optimal weight: 0.5980 chunk 27 optimal weight: 0.6980 chunk 98 optimal weight: 4.9990 chunk 106 optimal weight: 3.9990 chunk 87 optimal weight: 0.9990 chunk 97 optimal weight: 3.9990 chunk 33 optimal weight: 2.9990 chunk 78 optimal weight: 2.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 ASN D 44 GLN G 104 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8746 moved from start: 0.2872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 13673 Z= 0.322 Angle : 0.622 10.386 19721 Z= 0.369 Chirality : 0.039 0.152 2229 Planarity : 0.005 0.040 1477 Dihedral : 31.681 176.617 3903 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 2.24 % Allowed : 21.46 % Favored : 76.30 % 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: 1.47 (0.29), residues: 831 helix: 1.86 (0.22), residues: 551 sheet: -1.63 (1.18), residues: 21 loop : -0.71 (0.34), residues: 259 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 713 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 120 time to evaluate : 1.058 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 16 outliers final: 8 residues processed: 128 average time/residue: 1.7293 time to fit residues: 235.3979 Evaluate side-chains 122 residues out of total 713 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 114 time to evaluate : 0.968 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 4 residues processed: 5 average time/residue: 0.4360 time to fit residues: 3.8710 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 97 optimal weight: 3.9990 chunk 73 optimal weight: 6.9990 chunk 50 optimal weight: 0.6980 chunk 10 optimal weight: 0.5980 chunk 46 optimal weight: 0.2980 chunk 65 optimal weight: 1.9990 chunk 98 optimal weight: 4.9990 chunk 104 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 chunk 93 optimal weight: 0.8980 chunk 28 optimal weight: 1.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 44 GLN G 73 ASN G 104 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8696 moved from start: 0.3093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 13673 Z= 0.218 Angle : 0.568 10.601 19721 Z= 0.340 Chirality : 0.034 0.129 2229 Planarity : 0.004 0.041 1477 Dihedral : 31.198 178.503 3903 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 2.10 % Allowed : 21.04 % Favored : 76.86 % 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: 1.61 (0.29), residues: 831 helix: 1.92 (0.22), residues: 559 sheet: -2.01 (0.93), residues: 23 loop : -0.57 (0.35), residues: 249 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 713 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 123 time to evaluate : 1.065 Fit side-chains revert: symmetry clash outliers start: 15 outliers final: 7 residues processed: 131 average time/residue: 1.7486 time to fit residues: 243.9772 Evaluate side-chains 122 residues out of total 713 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 115 time to evaluate : 1.007 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 4 residues processed: 3 average time/residue: 0.4397 time to fit residues: 2.8218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 86 optimal weight: 0.0870 chunk 59 optimal weight: 2.9990 chunk 1 optimal weight: 0.9980 chunk 77 optimal weight: 2.9990 chunk 43 optimal weight: 0.4980 chunk 89 optimal weight: 3.9990 chunk 72 optimal weight: 5.9990 chunk 0 optimal weight: 4.9990 chunk 53 optimal weight: 7.9990 chunk 93 optimal weight: 0.7980 chunk 26 optimal weight: 0.8980 overall best weight: 0.6558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 104 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8677 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 : 0.003 0.047 13673 Z= 0.192 Angle : 0.553 8.445 19721 Z= 0.331 Chirality : 0.034 0.129 2229 Planarity : 0.004 0.054 1477 Dihedral : 31.119 178.836 3903 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 1.82 % Allowed : 21.88 % Favored : 76.30 % 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: 1.81 (0.29), residues: 831 helix: 2.04 (0.22), residues: 558 sheet: -1.93 (0.89), residues: 23 loop : -0.38 (0.35), residues: 250 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 713 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 117 time to evaluate : 0.994 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 9 residues processed: 125 average time/residue: 1.6736 time to fit residues: 223.3706 Evaluate side-chains 125 residues out of total 713 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 116 time to evaluate : 1.066 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 5 residues processed: 4 average time/residue: 0.4355 time to fit residues: 3.2992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/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-1.21rc1-5144/modules/cctbx_project/iotbx/cli_parser.py", line 931, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/phenix/phenix/programs/real_space_refine.py", line 191, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 297, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 673, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 737, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/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-1.21rc1-5144/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-1.21rc1-5144/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-1.21rc1-5144/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/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-1.21rc1-5144/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-1.21rc1-5144/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/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-1.21rc1-5144/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-1.21rc1-5144/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-1.21rc1-5144/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-1.21rc1-5144/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: 52.3652 > 50: distance: 2 - 26: 15.329 distance: 22 - 26: 11.887 distance: 26 - 27: 12.232 distance: 27 - 28: 11.733 distance: 27 - 30: 25.141 distance: 28 - 29: 31.713 distance: 28 - 31: 18.387 distance: 31 - 32: 16.234 distance: 32 - 33: 22.980 distance: 33 - 34: 23.415 distance: 33 - 35: 8.152 distance: 35 - 36: 5.322 distance: 36 - 37: 11.922 distance: 36 - 39: 22.256 distance: 37 - 38: 14.483 distance: 37 - 43: 25.482 distance: 39 - 40: 13.391 distance: 40 - 41: 5.163 distance: 40 - 42: 5.703 distance: 43 - 44: 9.595 distance: 44 - 45: 23.167 distance: 44 - 47: 13.118 distance: 45 - 46: 25.614 distance: 45 - 52: 10.734 distance: 47 - 48: 8.319 distance: 48 - 49: 10.272 distance: 49 - 50: 4.886 distance: 49 - 51: 5.371 distance: 52 - 53: 3.867 distance: 53 - 54: 8.110 distance: 53 - 56: 25.488 distance: 54 - 55: 13.074 distance: 54 - 63: 10.907 distance: 56 - 57: 12.058 distance: 57 - 58: 13.204 distance: 57 - 59: 10.237 distance: 58 - 60: 4.237 distance: 59 - 61: 9.024 distance: 60 - 62: 6.477 distance: 61 - 62: 7.086 distance: 63 - 64: 9.365 distance: 63 - 69: 15.372 distance: 64 - 65: 11.707 distance: 64 - 67: 18.325 distance: 65 - 66: 19.492 distance: 65 - 70: 6.285 distance: 67 - 68: 21.392 distance: 68 - 69: 24.151 distance: 70 - 71: 3.350 distance: 71 - 72: 8.658 distance: 72 - 73: 12.055 distance: 72 - 77: 10.109 distance: 73 - 99: 15.848 distance: 74 - 75: 5.791 distance: 74 - 76: 7.175 distance: 77 - 78: 14.490 distance: 78 - 79: 11.851 distance: 79 - 80: 4.205 distance: 79 - 81: 8.093 distance: 80 - 105: 8.891 distance: 81 - 82: 8.248 distance: 82 - 83: 3.848 distance: 82 - 85: 3.161 distance: 83 - 84: 4.945 distance: 83 - 92: 9.496 distance: 85 - 86: 10.400 distance: 87 - 88: 5.145 distance: 92 - 93: 7.367 distance: 93 - 94: 7.406 distance: 93 - 96: 5.541 distance: 94 - 95: 6.782 distance: 94 - 99: 5.240 distance: 95 - 122: 9.421 distance: 96 - 97: 8.960 distance: 96 - 98: 3.156