Starting phenix.real_space_refine (version: 1.21rc1) on Wed May 3 11:43:54 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6s5t_10100/05_2023/6s5t_10100_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6s5t_10100/05_2023/6s5t_10100.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.15 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6s5t_10100/05_2023/6s5t_10100.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6s5t_10100/05_2023/6s5t_10100.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6s5t_10100/05_2023/6s5t_10100_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6s5t_10100/05_2023/6s5t_10100_updated.pdb" } resolution = 4.15 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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= 0.026 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 3 5.49 5 S 22 5.16 5 C 4429 2.51 5 N 1186 2.21 5 O 1318 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 237": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 262": "NH1" <-> "NH2" Residue "A GLU 294": "OE1" <-> "OE2" Residue "A GLU 317": "OE1" <-> "OE2" Residue "A GLU 329": "OE1" <-> "OE2" Residue "A GLU 414": "OE1" <-> "OE2" Residue "A GLU 691": "OE1" <-> "OE2" Residue "A GLU 705": "OE1" <-> "OE2" Residue "A GLU 709": "OE1" <-> "OE2" Residue "A GLU 740": "OE1" <-> "OE2" Residue "A GLU 786": "OE1" <-> "OE2" Residue "A GLU 847": "OE1" <-> "OE2" Residue "B GLU 105": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/chem_data/mon_lib" Total number of atoms: 6958 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 5977 Number of conformers: 1 Conformer: "" Number of residues, atoms: 752, 5977 Classifications: {'peptide': 752} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 43} Link IDs: {'PTRANS': 31, 'TRANS': 720} Unresolved non-hydrogen bonds: 160 Unresolved non-hydrogen angles: 193 Unresolved non-hydrogen dihedrals: 129 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 4, 'ASN:plan1': 1, 'ASP:plan': 8, 'PHE:plan': 1, 'GLU:plan': 10, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 104 Chain: "B" Number of atoms: 950 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 950 Classifications: {'peptide': 144} Incomplete info: {'truncation_to_alanine': 50} Link IDs: {'PTRANS': 2, 'TRANS': 141} Unresolved non-hydrogen bonds: 193 Unresolved non-hydrogen angles: 243 Unresolved non-hydrogen dihedrals: 153 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 2, 'ASN:plan1': 4, 'ASP:plan': 10, 'PHE:plan': 2, 'GLU:plan': 13, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 148 Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ANP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.11, per 1000 atoms: 0.59 Number of scatterers: 6958 At special positions: 0 Unit cell: (101.76, 106.56, 86.4, 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 22 16.00 P 3 15.00 O 1318 8.00 N 1186 7.00 C 4429 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: 2.58 Conformation dependent library (CDL) restraints added in 1.0 seconds 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1704 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 40 helices and 6 sheets defined 51.2% alpha, 5.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.81 Creating SS restraints... Processing helix chain 'A' and resid 136 through 157 Processing helix chain 'A' and resid 165 through 181 Processing helix chain 'A' and resid 185 through 205 Proline residue: A 197 - end of helix removed outlier: 3.794A pdb=" N SER A 204 " --> pdb=" O THR A 200 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 219 removed outlier: 3.802A pdb=" N GLU A 218 " --> pdb=" O ASN A 214 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N LYS A 219 " --> pdb=" O GLU A 215 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 234 Processing helix chain 'A' and resid 237 through 245 Processing helix chain 'A' and resid 252 through 260 removed outlier: 3.566A pdb=" N LYS A 260 " --> pdb=" O ALA A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 268 No H-bonds generated for 'chain 'A' and resid 266 through 268' Processing helix chain 'A' and resid 271 through 280 Processing helix chain 'A' and resid 304 through 312 removed outlier: 4.663A pdb=" N ARG A 312 " --> pdb=" O ASN A 308 " (cutoff:3.500A) Processing helix chain 'A' and resid 343 through 345 No H-bonds generated for 'chain 'A' and resid 343 through 345' Processing helix chain 'A' and resid 375 through 390 Processing helix chain 'A' and resid 392 through 395 No H-bonds generated for 'chain 'A' and resid 392 through 395' Processing helix chain 'A' and resid 412 through 421 removed outlier: 3.851A pdb=" N ARG A 420 " --> pdb=" O LEU A 416 " (cutoff:3.500A) removed outlier: 5.281A pdb=" N GLY A 421 " --> pdb=" O GLU A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 425 through 431 Processing helix chain 'A' and resid 447 through 449 No H-bonds generated for 'chain 'A' and resid 447 through 449' Processing helix chain 'A' and resid 460 through 480 removed outlier: 3.589A pdb=" N GLU A 480 " --> pdb=" O VAL A 476 " (cutoff:3.500A) Processing helix chain 'A' and resid 526 through 529 No H-bonds generated for 'chain 'A' and resid 526 through 529' Processing helix chain 'A' and resid 549 through 552 Processing helix chain 'A' and resid 557 through 562 Processing helix chain 'A' and resid 564 through 567 No H-bonds generated for 'chain 'A' and resid 564 through 567' Processing helix chain 'A' and resid 573 through 575 No H-bonds generated for 'chain 'A' and resid 573 through 575' Processing helix chain 'A' and resid 588 through 622 removed outlier: 3.644A pdb=" N ARG A 592 " --> pdb=" O GLY A 589 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N PHE A 594 " --> pdb=" O ARG A 591 " (cutoff:3.500A) removed outlier: 5.275A pdb=" N GLY A 595 " --> pdb=" O ARG A 592 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ASN A 596 " --> pdb=" O LEU A 593 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LEU A 598 " --> pdb=" O GLY A 595 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N LEU A 600 " --> pdb=" O TYR A 597 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N ASN A 601 " --> pdb=" O LEU A 598 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ILE A 603 " --> pdb=" O LEU A 600 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ALA A 604 " --> pdb=" O ASN A 601 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N LEU A 607 " --> pdb=" O ALA A 604 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ILE A 610 " --> pdb=" O LEU A 607 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N THR A 613 " --> pdb=" O ILE A 610 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N TYR A 617 " --> pdb=" O LEU A 614 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N GLY A 618 " --> pdb=" O GLY A 615 " (cutoff:3.500A) Processing helix chain 'A' and resid 628 through 653 removed outlier: 3.645A pdb=" N GLU A 637 " --> pdb=" O ALA A 633 " (cutoff:3.500A) Processing helix chain 'A' and resid 658 through 666 removed outlier: 3.551A pdb=" N THR A 663 " --> pdb=" O SER A 659 " (cutoff:3.500A) Processing helix chain 'A' and resid 671 through 681 Processing helix chain 'A' and resid 686 through 688 No H-bonds generated for 'chain 'A' and resid 686 through 688' Processing helix chain 'A' and resid 691 through 701 Processing helix chain 'A' and resid 739 through 773 removed outlier: 3.695A pdb=" N LEU A 751 " --> pdb=" O ALA A 747 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N LEU A 758 " --> pdb=" O GLY A 754 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N PHE A 763 " --> pdb=" O ASP A 759 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LYS A 764 " --> pdb=" O LYS A 760 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LYS A 771 " --> pdb=" O GLU A 767 " (cutoff:3.500A) Processing helix chain 'A' and resid 781 through 792 Processing helix chain 'A' and resid 801 through 816 Processing helix chain 'A' and resid 827 through 845 Processing helix chain 'B' and resid 7 through 19 Processing helix chain 'B' and resid 30 through 39 removed outlier: 5.737A pdb=" N GLY B 34 " --> pdb=" O LYS B 31 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N MET B 37 " --> pdb=" O GLY B 34 " (cutoff:3.500A) Processing helix chain 'B' and resid 46 through 56 Processing helix chain 'B' and resid 66 through 76 Processing helix chain 'B' and resid 83 through 91 Processing helix chain 'B' and resid 103 through 112 Processing helix chain 'B' and resid 119 through 127 Processing helix chain 'B' and resid 139 through 145 Processing sheet with id= A, first strand: chain 'A' and resid 105 through 109 Processing sheet with id= B, first strand: chain 'A' and resid 121 through 124 Processing sheet with id= C, first strand: chain 'A' and resid 131 through 133 removed outlier: 5.833A pdb=" N ALA A 583 " --> pdb=" O LYS A 132 " (cutoff:3.500A) No H-bonds generated for sheet with id= C Processing sheet with id= D, first strand: chain 'A' and resid 291 through 294 Processing sheet with id= E, first strand: chain 'A' and resid 353 through 357 removed outlier: 3.769A pdb=" N GLY A 406 " --> pdb=" O VAL A 442 " (cutoff:3.500A) removed outlier: 5.920A pdb=" N LYS A 444 " --> pdb=" O PRO A 404 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 409 through 411 299 hydrogen bonds defined for protein. 813 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: 1.68 Time building geometry restraints manager: 2.83 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2242 1.34 - 1.46: 1722 1.46 - 1.58: 3098 1.58 - 1.70: 5 1.70 - 1.82: 41 Bond restraints: 7108 Sorted by residual: bond pdb=" N3B ANP A 901 " pdb=" PG ANP A 901 " ideal model delta sigma weight residual 1.795 1.641 0.154 2.00e-02 2.50e+03 5.96e+01 bond pdb=" O3A ANP A 901 " pdb=" PB ANP A 901 " ideal model delta sigma weight residual 1.700 1.604 0.096 2.00e-02 2.50e+03 2.31e+01 bond pdb=" O5' ANP A 901 " pdb=" PA ANP A 901 " ideal model delta sigma weight residual 1.655 1.602 0.053 2.00e-02 2.50e+03 7.06e+00 bond pdb=" C TYR A 222 " pdb=" N PRO A 223 " ideal model delta sigma weight residual 1.334 1.355 -0.021 8.40e-03 1.42e+04 6.44e+00 bond pdb=" C LEU A 117 " pdb=" N PRO A 118 " ideal model delta sigma weight residual 1.329 1.357 -0.028 1.18e-02 7.18e+03 5.65e+00 ... (remaining 7103 not shown) Histogram of bond angle deviations from ideal: 100.47 - 107.28: 210 107.28 - 114.09: 3725 114.09 - 120.89: 3355 120.89 - 127.70: 2314 127.70 - 134.51: 42 Bond angle restraints: 9646 Sorted by residual: angle pdb=" CA PHE A 269 " pdb=" CB PHE A 269 " pdb=" CG PHE A 269 " ideal model delta sigma weight residual 113.80 118.84 -5.04 1.00e+00 1.00e+00 2.54e+01 angle pdb=" C THR A 654 " pdb=" CA THR A 654 " pdb=" CB THR A 654 " ideal model delta sigma weight residual 109.02 116.89 -7.87 1.68e+00 3.54e-01 2.19e+01 angle pdb=" CA ASP A 542 " pdb=" CB ASP A 542 " pdb=" CG ASP A 542 " ideal model delta sigma weight residual 112.60 117.26 -4.66 1.00e+00 1.00e+00 2.17e+01 angle pdb=" C THR A 451 " pdb=" CA THR A 451 " pdb=" CB THR A 451 " ideal model delta sigma weight residual 110.19 116.95 -6.76 1.62e+00 3.81e-01 1.74e+01 angle pdb=" C ASP A 542 " pdb=" CA ASP A 542 " pdb=" CB ASP A 542 " ideal model delta sigma weight residual 110.42 118.64 -8.22 1.99e+00 2.53e-01 1.71e+01 ... (remaining 9641 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.54: 4108 35.54 - 71.08: 143 71.08 - 106.63: 4 106.63 - 142.17: 0 142.17 - 177.71: 1 Dihedral angle restraints: 4256 sinusoidal: 1621 harmonic: 2635 Sorted by residual: dihedral pdb=" O1B ANP A 901 " pdb=" N3B ANP A 901 " pdb=" PB ANP A 901 " pdb=" PG ANP A 901 " ideal model delta sinusoidal sigma weight residual 35.15 -142.56 177.71 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" CA TYR A 222 " pdb=" C TYR A 222 " pdb=" N PRO A 223 " pdb=" CA PRO A 223 " ideal model delta harmonic sigma weight residual -180.00 -157.03 -22.97 0 5.00e+00 4.00e-02 2.11e+01 dihedral pdb=" C THR A 654 " pdb=" N THR A 654 " pdb=" CA THR A 654 " pdb=" CB THR A 654 " ideal model delta harmonic sigma weight residual -122.00 -133.28 11.28 0 2.50e+00 1.60e-01 2.03e+01 ... (remaining 4253 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.081: 681 0.081 - 0.162: 307 0.162 - 0.242: 90 0.242 - 0.323: 11 0.323 - 0.404: 2 Chirality restraints: 1091 Sorted by residual: chirality pdb=" CA ASN A 271 " pdb=" N ASN A 271 " pdb=" C ASN A 271 " pdb=" CB ASN A 271 " both_signs ideal model delta sigma weight residual False 2.51 2.11 0.40 2.00e-01 2.50e+01 4.08e+00 chirality pdb=" CA THR A 654 " pdb=" N THR A 654 " pdb=" C THR A 654 " pdb=" CB THR A 654 " both_signs ideal model delta sigma weight residual False 2.53 2.15 0.37 2.00e-01 2.50e+01 3.50e+00 chirality pdb=" CA ASP A 542 " pdb=" N ASP A 542 " pdb=" C ASP A 542 " pdb=" CB ASP A 542 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.31 2.00e-01 2.50e+01 2.33e+00 ... (remaining 1088 not shown) Planarity restraints: 1236 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 606 " -0.013 2.00e-02 2.50e+03 7.66e-03 1.17e+00 pdb=" CG TYR A 606 " 0.015 2.00e-02 2.50e+03 pdb=" CD1 TYR A 606 " 0.002 2.00e-02 2.50e+03 pdb=" CD2 TYR A 606 " 0.005 2.00e-02 2.50e+03 pdb=" CE1 TYR A 606 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR A 606 " -0.004 2.00e-02 2.50e+03 pdb=" CZ TYR A 606 " -0.002 2.00e-02 2.50e+03 pdb=" OH TYR A 606 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 393 " 0.068 9.50e-02 1.11e+02 3.13e-02 1.07e+00 pdb=" NE ARG A 393 " -0.000 2.00e-02 2.50e+03 pdb=" CZ ARG A 393 " -0.013 2.00e-02 2.50e+03 pdb=" NH1 ARG A 393 " 0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG A 393 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 242 " 0.005 2.00e-02 2.50e+03 1.02e-02 1.04e+00 pdb=" C ILE A 242 " -0.018 2.00e-02 2.50e+03 pdb=" O ILE A 242 " 0.007 2.00e-02 2.50e+03 pdb=" N HIS A 243 " 0.006 2.00e-02 2.50e+03 ... (remaining 1233 not shown) Histogram of nonbonded interaction distances: 2.45 - 2.94: 2648 2.94 - 3.43: 7015 3.43 - 3.92: 11158 3.92 - 4.41: 12126 4.41 - 4.90: 19835 Nonbonded interactions: 52782 Sorted by model distance: nonbonded pdb=" O GLN A 350 " pdb=" OG1 THR A 353 " model vdw 2.450 2.440 nonbonded pdb=" ND2 ASN A 470 " pdb=" O ARG A 536 " model vdw 2.525 2.520 nonbonded pdb=" NE2 GLN A 842 " pdb=" O GLU B 115 " model vdw 2.525 2.520 nonbonded pdb=" O TRP A 845 " pdb=" N GLU A 847 " model vdw 2.525 2.520 nonbonded pdb=" O GLU A 294 " pdb=" OG SER A 297 " model vdw 2.526 2.440 ... (remaining 52777 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.140 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: 1.540 Check model and map are aligned: 0.100 Set scattering table: 0.060 Process input model: 20.310 Find NCS groups from input model: 0.180 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:2.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 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 : 0.007 0.154 7108 Z= 0.461 Angle : 1.477 10.703 9646 Z= 0.994 Chirality : 0.094 0.404 1091 Planarity : 0.003 0.031 1236 Dihedral : 17.310 177.709 2552 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.56 % Allowed : 7.06 % Favored : 92.38 % Rotamer Outliers : 3.93 % Cbeta Deviations : 0.35 % 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: -4.05 (0.22), residues: 892 helix: -2.73 (0.17), residues: 498 sheet: -0.64 (0.92), residues: 32 loop : -2.63 (0.26), residues: 362 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 805 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 175 time to evaluate : 0.835 Fit side-chains outliers start: 28 outliers final: 8 residues processed: 196 average time/residue: 0.1993 time to fit residues: 51.3944 Evaluate side-chains 131 residues out of total 805 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 123 time to evaluate : 0.836 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.0666 time to fit residues: 2.1447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 75 optimal weight: 8.9990 chunk 67 optimal weight: 7.9990 chunk 37 optimal weight: 3.9990 chunk 23 optimal weight: 10.0000 chunk 45 optimal weight: 6.9990 chunk 36 optimal weight: 2.9990 chunk 69 optimal weight: 3.9990 chunk 26 optimal weight: 8.9990 chunk 42 optimal weight: 0.0770 chunk 51 optimal weight: 0.6980 chunk 80 optimal weight: 6.9990 overall best weight: 2.3544 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 166 GLN A 189 ASN ** A 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 271 ASN A 308 ASN A 517 GLN ** B 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.2577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.031 7108 Z= 0.243 Angle : 0.582 5.967 9646 Z= 0.305 Chirality : 0.040 0.146 1091 Planarity : 0.004 0.045 1236 Dihedral : 8.113 177.910 973 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer Outliers : 0.14 % 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: -1.78 (0.26), residues: 892 helix: -0.62 (0.23), residues: 491 sheet: -0.59 (0.93), residues: 33 loop : -1.94 (0.29), residues: 368 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 805 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 163 time to evaluate : 0.785 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 164 average time/residue: 0.1891 time to fit residues: 41.1731 Evaluate side-chains 114 residues out of total 805 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 114 time to evaluate : 0.761 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.0715 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/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-1.21rc1-4953/modules/cctbx_project/iotbx/cli_parser.py", line 872, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/phenix/phenix/programs/real_space_refine.py", line 192, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/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-1.21rc1-4953/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/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-1.21rc1-4953/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-1.21rc1-4953/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-1.21rc1-4953/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-1.21rc1-4953/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-1.21rc1-4953/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/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-1.21rc1-4953/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-1.21rc1-4953/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/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-1.21rc1-4953/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-1.21rc1-4953/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-1.21rc1-4953/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-1.21rc1-4953/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: 59.1316 > 50: distance: 27 - 32: 4.775 distance: 32 - 33: 6.410 distance: 33 - 34: 14.807 distance: 33 - 36: 7.105 distance: 34 - 35: 5.618 distance: 34 - 43: 12.028 distance: 36 - 37: 7.942 distance: 38 - 39: 5.534 distance: 39 - 40: 7.680 distance: 40 - 41: 7.508 distance: 40 - 42: 11.131 distance: 43 - 44: 11.313 distance: 44 - 45: 25.719 distance: 44 - 47: 8.343 distance: 45 - 46: 18.448 distance: 45 - 51: 47.119 distance: 47 - 48: 12.483 distance: 47 - 49: 29.911 distance: 48 - 50: 16.814 distance: 51 - 52: 6.771 distance: 52 - 53: 16.879 distance: 52 - 55: 27.578 distance: 53 - 54: 19.546 distance: 53 - 60: 17.857 distance: 55 - 56: 32.655 distance: 56 - 57: 26.979 distance: 57 - 58: 9.091 distance: 57 - 59: 10.977 distance: 60 - 61: 23.718 distance: 61 - 62: 41.266 distance: 62 - 63: 21.628 distance: 62 - 64: 27.030 distance: 64 - 65: 3.980 distance: 65 - 68: 9.708 distance: 66 - 75: 23.274 distance: 68 - 69: 5.462 distance: 69 - 70: 11.063 distance: 70 - 71: 10.052 distance: 71 - 72: 6.671 distance: 72 - 73: 3.235 distance: 72 - 74: 10.316 distance: 75 - 76: 7.631 distance: 76 - 77: 9.915 distance: 76 - 79: 9.689 distance: 77 - 78: 18.760 distance: 77 - 82: 10.692 distance: 79 - 80: 15.767 distance: 79 - 81: 14.032 distance: 82 - 83: 16.664 distance: 82 - 145: 12.059 distance: 83 - 84: 7.390 distance: 83 - 86: 4.318 distance: 84 - 85: 10.422 distance: 84 - 90: 10.696 distance: 85 - 142: 5.977 distance: 86 - 87: 7.610 distance: 87 - 88: 11.647 distance: 87 - 89: 9.487 distance: 90 - 91: 4.284 distance: 91 - 92: 19.517 distance: 91 - 94: 10.569 distance: 92 - 93: 30.776 distance: 92 - 98: 18.805 distance: 94 - 95: 17.736 distance: 95 - 96: 22.015 distance: 95 - 97: 10.160 distance: 98 - 134: 12.485 distance: 99 - 100: 10.996 distance: 99 - 102: 14.242 distance: 100 - 101: 7.086 distance: 100 - 109: 8.807 distance: 101 - 131: 16.930 distance: 102 - 103: 4.060 distance: 103 - 104: 10.594 distance: 103 - 105: 21.565 distance: 104 - 106: 11.181 distance: 105 - 107: 11.027 distance: 106 - 108: 16.925 distance: 107 - 108: 19.392 distance: 109 - 110: 12.936 distance: 110 - 111: 5.221 distance: 110 - 113: 13.309 distance: 111 - 112: 7.727 distance: 111 - 115: 7.795 distance: 113 - 114: 8.732