Starting phenix.real_space_refine on Fri Dec 8 03:31:47 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x7t_33047/12_2023/7x7t_33047.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x7t_33047/12_2023/7x7t_33047.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.48 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x7t_33047/12_2023/7x7t_33047.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x7t_33047/12_2023/7x7t_33047.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x7t_33047/12_2023/7x7t_33047.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x7t_33047/12_2023/7x7t_33047.pdb" } resolution = 3.48 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.016 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 25 5.16 5 C 4323 2.51 5 N 1123 2.21 5 O 1344 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "G ARG 357": "NH1" <-> "NH2" Residue "G ARG 408": "NH1" <-> "NH2" Residue "L GLU 85": "OE1" <-> "OE2" Residue "H GLU 82": "OE1" <-> "OE2" Residue "A GLU 10": "OE1" <-> "OE2" Residue "D GLU 81": "OE1" <-> "OE2" Residue "C ARG 38": "NH1" <-> "NH2" Residue "C GLU 89": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 6815 Number of models: 1 Model: "" Number of chains: 8 Chain: "G" Number of atoms: 1494 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 1494 Classifications: {'peptide': 187} Link IDs: {'PTRANS': 9, 'TRANS': 177} Chain breaks: 1 Chain: "L" Number of atoms: 853 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 853 Classifications: {'peptide': 111} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 103} Chain: "H" Number of atoms: 946 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 946 Classifications: {'peptide': 121} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 117} Chain: "B" Number of atoms: 827 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 827 Classifications: {'peptide': 107} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 103} Chain: "A" Number of atoms: 929 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 929 Classifications: {'peptide': 119} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 115} Chain: "D" Number of atoms: 831 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 831 Classifications: {'peptide': 107} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 102} Chain: "C" Number of atoms: 921 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 921 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 3, 'TRANS': 115} Chain: "G" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 4.38, per 1000 atoms: 0.64 Number of scatterers: 6815 At special positions: 0 Unit cell: (84.802, 94.138, 112.81, 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 25 16.00 O 1344 8.00 N 1123 7.00 C 4323 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS G 336 " - pdb=" SG CYS G 361 " distance=1.57 Simple disulfide: pdb=" SG CYS G 379 " - pdb=" SG CYS G 432 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 92 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS B 23 " - pdb=" SG CYS B 88 " distance=2.04 Simple disulfide: pdb=" SG CYS A 22 " - pdb=" SG CYS A 96 " distance=2.03 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 88 " distance=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 96 " distance=2.02 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 Links applied NAG-ASN " NAG G 601 " - " ASN G 343 " Time building additional restraints: 2.37 Conformation dependent library (CDL) restraints added in 1.5 seconds 1710 Ramachandran restraints generated. 855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1580 Finding SS restraints... Secondary structure from input PDB file: 10 helices and 24 sheets defined 5.4% alpha, 26.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.03 Creating SS restraints... Processing helix chain 'G' and resid 365 through 370 removed outlier: 3.649A pdb=" N ASN G 370 " --> pdb=" O SER G 366 " (cutoff:3.500A) Processing helix chain 'G' and resid 386 through 390 removed outlier: 4.116A pdb=" N LEU G 390 " --> pdb=" O LEU G 387 " (cutoff:3.500A) Processing helix chain 'G' and resid 405 through 407 No H-bonds generated for 'chain 'G' and resid 405 through 407' Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.719A pdb=" N TYR H 32 " --> pdb=" O PHE H 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 62 through 65 removed outlier: 3.715A pdb=" N GLU H 65 " --> pdb=" O LEU H 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 62 through 65' Processing helix chain 'H' and resid 74 through 77 removed outlier: 3.617A pdb=" N ASN H 77 " --> pdb=" O LYS H 74 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 74 through 77' Processing helix chain 'B' and resid 79 through 83 removed outlier: 3.747A pdb=" N ILE B 83 " --> pdb=" O GLN B 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 28 through 32 Processing helix chain 'A' and resid 87 through 91 removed outlier: 3.663A pdb=" N SER A 91 " --> pdb=" O SER A 88 " (cutoff:3.500A) Processing helix chain 'C' and resid 28 through 32 removed outlier: 3.591A pdb=" N TYR C 32 " --> pdb=" O PHE C 29 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'G' and resid 356 through 358 removed outlier: 3.509A pdb=" N ILE G 402 " --> pdb=" O TYR G 508 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LEU G 513 " --> pdb=" O CYS G 432 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N THR G 376 " --> pdb=" O ALA G 435 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'G' and resid 473 through 474 removed outlier: 3.616A pdb=" N TYR G 473 " --> pdb=" O TYR G 489 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N TYR G 489 " --> pdb=" O TYR G 473 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'L' and resid 4 through 7 removed outlier: 3.649A pdb=" N SER L 7 " --> pdb=" O SER L 22 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N SER L 22 " --> pdb=" O SER L 7 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N ILE L 79 " --> pdb=" O ALA L 19 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'L' and resid 11 through 14 removed outlier: 3.997A pdb=" N THR L 106 " --> pdb=" O TYR L 90 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'L' and resid 39 through 41 removed outlier: 6.839A pdb=" N TRP L 39 " --> pdb=" O LEU L 51 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 3 through 6 removed outlier: 3.580A pdb=" N GLN H 3 " --> pdb=" O SER H 25 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N SER H 25 " --> pdb=" O GLN H 3 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N GLN H 5 " --> pdb=" O LYS H 23 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LYS H 23 " --> pdb=" O GLN H 5 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.679A pdb=" N THR H 115 " --> pdb=" O PHE H 94 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 18 through 19 Processing sheet with id=AA9, first strand: chain 'H' and resid 49 through 52 removed outlier: 3.769A pdb=" N GLY H 57 " --> pdb=" O ASP H 52 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'H' and resid 72 through 73 removed outlier: 3.800A pdb=" N ASP H 73 " --> pdb=" O THR H 78 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N THR H 78 " --> pdb=" O ASP H 73 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'B' and resid 19 through 24 removed outlier: 3.845A pdb=" N ASP B 70 " --> pdb=" O SER B 67 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N SER B 67 " --> pdb=" O ASP B 70 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 54 through 55 removed outlier: 6.783A pdb=" N LEU B 54 " --> pdb=" O TYR B 49 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N TRP B 35 " --> pdb=" O LEU B 47 " (cutoff:3.500A) removed outlier: 5.270A pdb=" N TYR B 49 " --> pdb=" O LEU B 33 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N LEU B 33 " --> pdb=" O TYR B 49 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N GLN B 90 " --> pdb=" O THR B 97 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N THR B 97 " --> pdb=" O GLN B 90 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 85 through 86 removed outlier: 3.673A pdb=" N TYR B 86 " --> pdb=" O THR B 102 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 3 through 6 removed outlier: 3.578A pdb=" N GLN A 3 " --> pdb=" O SER A 25 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 10 through 12 removed outlier: 3.586A pdb=" N GLN A 39 " --> pdb=" O VAL A 93 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N LYS A 38 " --> pdb=" O TRP A 47 " (cutoff:3.500A) removed outlier: 5.515A pdb=" N TRP A 47 " --> pdb=" O LYS A 38 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 10 through 12 Processing sheet with id=AB8, first strand: chain 'D' and resid 4 through 6 removed outlier: 3.833A pdb=" N VAL D 19 " --> pdb=" O ILE D 75 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N ASN D 70 " --> pdb=" O SER D 67 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N SER D 67 " --> pdb=" O ASN D 70 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 10 through 11 Processing sheet with id=AC1, first strand: chain 'D' and resid 45 through 46 Processing sheet with id=AC2, first strand: chain 'C' and resid 3 through 6 Processing sheet with id=AC3, first strand: chain 'C' and resid 10 through 11 Processing sheet with id=AC4, first strand: chain 'C' and resid 18 through 20 Processing sheet with id=AC5, first strand: chain 'C' and resid 49 through 51 Processing sheet with id=AC6, first strand: chain 'C' and resid 97 through 98 162 hydrogen bonds defined for protein. 363 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: 1.97 Time building geometry restraints manager: 2.56 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.29: 1107 1.29 - 1.42: 2023 1.42 - 1.55: 3825 1.55 - 1.68: 3 1.68 - 1.81: 30 Bond restraints: 6988 Sorted by residual: bond pdb=" C ASN G 334 " pdb=" O ASN G 334 " ideal model delta sigma weight residual 1.235 1.160 0.075 1.21e-02 6.83e+03 3.86e+01 bond pdb=" C GLN C 3 " pdb=" O GLN C 3 " ideal model delta sigma weight residual 1.236 1.302 -0.066 1.19e-02 7.06e+03 3.07e+01 bond pdb=" C LYS C 23 " pdb=" O LYS C 23 " ideal model delta sigma weight residual 1.235 1.299 -0.063 1.23e-02 6.61e+03 2.64e+01 bond pdb=" C LEU C 4 " pdb=" O LEU C 4 " ideal model delta sigma weight residual 1.236 1.289 -0.053 1.14e-02 7.69e+03 2.15e+01 bond pdb=" CA TRP C 47 " pdb=" C TRP C 47 " ideal model delta sigma weight residual 1.527 1.470 0.057 1.35e-02 5.49e+03 1.77e+01 ... (remaining 6983 not shown) Histogram of bond angle deviations from ideal: 93.91 - 102.00: 15 102.00 - 110.09: 1354 110.09 - 118.18: 3795 118.18 - 126.27: 4214 126.27 - 134.36: 118 Bond angle restraints: 9496 Sorted by residual: angle pdb=" N PHE G 338 " pdb=" CA PHE G 338 " pdb=" C PHE G 338 " ideal model delta sigma weight residual 112.92 98.64 14.28 1.23e+00 6.61e-01 1.35e+02 angle pdb=" N ILE D 29 " pdb=" CA ILE D 29 " pdb=" C ILE D 29 " ideal model delta sigma weight residual 108.11 93.91 14.20 1.40e+00 5.10e-01 1.03e+02 angle pdb=" N ASN L 35 " pdb=" CA ASN L 35 " pdb=" C ASN L 35 " ideal model delta sigma weight residual 110.17 96.65 13.52 1.61e+00 3.86e-01 7.05e+01 angle pdb=" N TRP C 47 " pdb=" CA TRP C 47 " pdb=" C TRP C 47 " ideal model delta sigma weight residual 110.53 120.04 -9.51 1.32e+00 5.74e-01 5.19e+01 angle pdb=" CA TYR L 91 " pdb=" C TYR L 91 " pdb=" O TYR L 91 " ideal model delta sigma weight residual 122.01 115.31 6.70 1.05e+00 9.07e-01 4.07e+01 ... (remaining 9491 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.03: 3682 17.03 - 34.06: 320 34.06 - 51.09: 48 51.09 - 68.12: 15 68.12 - 85.15: 7 Dihedral angle restraints: 4072 sinusoidal: 1566 harmonic: 2506 Sorted by residual: dihedral pdb=" C CYS G 336 " pdb=" N CYS G 336 " pdb=" CA CYS G 336 " pdb=" CB CYS G 336 " ideal model delta harmonic sigma weight residual -122.60 -108.63 -13.97 0 2.50e+00 1.60e-01 3.12e+01 dihedral pdb=" C THR A 113 " pdb=" N THR A 113 " pdb=" CA THR A 113 " pdb=" CB THR A 113 " ideal model delta harmonic sigma weight residual -122.00 -109.65 -12.35 0 2.50e+00 1.60e-01 2.44e+01 dihedral pdb=" CA ASN D 31 " pdb=" C ASN D 31 " pdb=" N TRP D 32 " pdb=" CA TRP D 32 " ideal model delta harmonic sigma weight residual 180.00 -155.69 -24.31 0 5.00e+00 4.00e-02 2.36e+01 ... (remaining 4069 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.090: 898 0.090 - 0.181: 100 0.181 - 0.271: 14 0.271 - 0.361: 4 0.361 - 0.451: 2 Chirality restraints: 1018 Sorted by residual: chirality pdb=" CA TYR D 91 " pdb=" N TYR D 91 " pdb=" C TYR D 91 " pdb=" CB TYR D 91 " both_signs ideal model delta sigma weight residual False 2.51 2.06 0.45 2.00e-01 2.50e+01 5.09e+00 chirality pdb=" CA TYR L 36 " pdb=" N TYR L 36 " pdb=" C TYR L 36 " pdb=" CB TYR L 36 " both_signs ideal model delta sigma weight residual False 2.51 2.11 0.40 2.00e-01 2.50e+01 3.99e+00 chirality pdb=" CA CYS G 336 " pdb=" N CYS G 336 " pdb=" C CYS G 336 " pdb=" CB CYS G 336 " both_signs ideal model delta sigma weight residual False 2.51 2.85 -0.34 2.00e-01 2.50e+01 2.83e+00 ... (remaining 1015 not shown) Planarity restraints: 1218 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA CYS G 336 " -0.013 2.00e-02 2.50e+03 2.62e-02 6.88e+00 pdb=" C CYS G 336 " 0.045 2.00e-02 2.50e+03 pdb=" O CYS G 336 " -0.017 2.00e-02 2.50e+03 pdb=" N PRO G 337 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU G 335 " 0.013 2.00e-02 2.50e+03 2.53e-02 6.40e+00 pdb=" C LEU G 335 " -0.044 2.00e-02 2.50e+03 pdb=" O LEU G 335 " 0.016 2.00e-02 2.50e+03 pdb=" N CYS G 336 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN B 77 " -0.013 2.00e-02 2.50e+03 2.52e-02 6.34e+00 pdb=" C ASN B 77 " 0.044 2.00e-02 2.50e+03 pdb=" O ASN B 77 " -0.016 2.00e-02 2.50e+03 pdb=" N LEU B 78 " -0.015 2.00e-02 2.50e+03 ... (remaining 1215 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 418 2.72 - 3.26: 6442 3.26 - 3.81: 10227 3.81 - 4.35: 13116 4.35 - 4.90: 23035 Nonbonded interactions: 53238 Sorted by model distance: nonbonded pdb=" O ALA A 24 " pdb=" OG SER A 77 " model vdw 2.174 2.440 nonbonded pdb=" OD2 ASP C 73 " pdb=" OG SER C 75 " model vdw 2.246 2.440 nonbonded pdb=" NE2 GLN B 38 " pdb=" OE1 GLN A 39 " model vdw 2.304 2.520 nonbonded pdb=" O SER D 60 " pdb=" OG SER D 60 " model vdw 2.323 2.440 nonbonded pdb=" OH TYR C 60 " pdb=" N LEU C 70 " model vdw 2.332 2.520 ... (remaining 53233 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=0.67 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: 3.750 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: 13.300 Check model and map are aligned: 0.100 Set scattering table: 0.070 Process input model: 23.040 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.030 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:2.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5886 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 0.075 6988 Z= 0.442 Angle : 1.038 14.279 9496 Z= 0.644 Chirality : 0.063 0.451 1018 Planarity : 0.006 0.058 1217 Dihedral : 13.408 85.150 2468 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.96 % Favored : 93.92 % Rotamer: Outliers : 0.14 % Allowed : 3.95 % Favored : 95.91 % Cbeta Deviations : 0.38 % Peptide Plane: Cis-proline : 6.25 % 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: -4.53 (0.24), residues: 855 helix: -5.31 (0.19), residues: 27 sheet: -2.86 (0.26), residues: 317 loop : -3.06 (0.23), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.003 TRP C 47 HIS 0.003 0.001 HIS B 55 PHE 0.027 0.002 PHE A 29 TYR 0.025 0.002 TYR D 91 ARG 0.002 0.000 ARG G 466 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1710 Ramachandran restraints generated. 855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1710 Ramachandran restraints generated. 855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 734 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 196 time to evaluate : 0.815 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 196 average time/residue: 0.1902 time to fit residues: 49.5419 Evaluate side-chains 153 residues out of total 734 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 153 time to evaluate : 0.763 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.0556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 70 optimal weight: 0.5980 chunk 62 optimal weight: 0.5980 chunk 34 optimal weight: 4.9990 chunk 21 optimal weight: 1.9990 chunk 42 optimal weight: 5.9990 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 0.7980 chunk 25 optimal weight: 0.8980 chunk 39 optimal weight: 0.8980 chunk 48 optimal weight: 0.8980 chunk 75 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 34 ASN D 38 GLN ** C 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 39 GLN ** C 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5856 moved from start: 0.1654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 6988 Z= 0.244 Angle : 0.633 11.714 9496 Z= 0.324 Chirality : 0.044 0.154 1018 Planarity : 0.004 0.045 1217 Dihedral : 5.858 37.853 980 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.73 % Favored : 94.27 % Rotamer: Outliers : 2.45 % Allowed : 12.26 % Favored : 85.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: -3.90 (0.25), residues: 855 helix: -5.21 (0.24), residues: 26 sheet: -2.56 (0.26), residues: 319 loop : -2.50 (0.24), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP D 35 HIS 0.003 0.001 HIS L 94 PHE 0.018 0.002 PHE G 490 TYR 0.017 0.001 TYR D 91 ARG 0.002 0.000 ARG A 63 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1710 Ramachandran restraints generated. 855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1710 Ramachandran restraints generated. 855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 734 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 150 time to evaluate : 0.708 Fit side-chains outliers start: 18 outliers final: 15 residues processed: 157 average time/residue: 0.1701 time to fit residues: 36.2004 Evaluate side-chains 155 residues out of total 734 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 140 time to evaluate : 0.692 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.0645 time to fit residues: 2.6744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 41 optimal weight: 4.9990 chunk 23 optimal weight: 2.9990 chunk 62 optimal weight: 3.9990 chunk 51 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 75 optimal weight: 0.5980 chunk 81 optimal weight: 0.7980 chunk 67 optimal weight: 4.9990 chunk 74 optimal weight: 0.9990 chunk 25 optimal weight: 0.9980 chunk 60 optimal weight: 1.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 77 ASN D 38 GLN D 42 ASN ** C 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 39 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5882 moved from start: 0.1946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 6988 Z= 0.316 Angle : 0.645 13.058 9496 Z= 0.326 Chirality : 0.044 0.157 1018 Planarity : 0.004 0.039 1217 Dihedral : 5.687 30.368 980 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.73 % Favored : 94.27 % Rotamer: Outliers : 1.50 % Allowed : 16.62 % Favored : 81.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: -3.50 (0.26), residues: 855 helix: -5.16 (0.25), residues: 26 sheet: -2.27 (0.26), residues: 340 loop : -2.19 (0.25), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP G 436 HIS 0.008 0.002 HIS C 82 PHE 0.020 0.002 PHE G 377 TYR 0.017 0.002 TYR D 91 ARG 0.002 0.000 ARG G 466 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1710 Ramachandran restraints generated. 855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1710 Ramachandran restraints generated. 855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 734 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 140 time to evaluate : 1.969 Fit side-chains outliers start: 11 outliers final: 6 residues processed: 145 average time/residue: 0.2061 time to fit residues: 41.2478 Evaluate side-chains 140 residues out of total 734 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 134 time to evaluate : 0.765 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0697 time to fit residues: 1.7959 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 74 optimal weight: 0.6980 chunk 56 optimal weight: 0.9980 chunk 39 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 36 optimal weight: 0.0980 chunk 50 optimal weight: 0.8980 chunk 75 optimal weight: 0.9980 chunk 80 optimal weight: 3.9990 chunk 71 optimal weight: 0.5980 chunk 21 optimal weight: 1.9990 chunk 66 optimal weight: 0.6980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 394 ASN ** G 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 38 GLN D 42 ASN ** C 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 39 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5851 moved from start: 0.2253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6988 Z= 0.207 Angle : 0.586 11.871 9496 Z= 0.292 Chirality : 0.042 0.200 1018 Planarity : 0.004 0.041 1217 Dihedral : 5.254 27.360 980 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 1.77 % Allowed : 17.44 % Favored : 80.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.96 (0.26), residues: 855 helix: -5.03 (0.29), residues: 26 sheet: -1.76 (0.27), residues: 336 loop : -1.94 (0.25), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP G 436 HIS 0.006 0.001 HIS C 82 PHE 0.019 0.002 PHE G 490 TYR 0.018 0.001 TYR C 32 ARG 0.002 0.000 ARG G 408 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1710 Ramachandran restraints generated. 855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1710 Ramachandran restraints generated. 855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 734 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 138 time to evaluate : 0.754 Fit side-chains outliers start: 13 outliers final: 10 residues processed: 143 average time/residue: 0.1725 time to fit residues: 33.8469 Evaluate side-chains 143 residues out of total 734 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 133 time to evaluate : 0.720 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.0652 time to fit residues: 2.1843 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 45 optimal weight: 0.6980 chunk 1 optimal weight: 0.9980 chunk 59 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 chunk 68 optimal weight: 4.9990 chunk 55 optimal weight: 3.9990 chunk 0 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 72 optimal weight: 3.9990 chunk 20 optimal weight: 1.9990 chunk 26 optimal weight: 3.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 370 ASN ** G 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 111 GLN D 38 GLN ** C 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 39 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5906 moved from start: 0.2334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.073 6988 Z= 0.419 Angle : 0.681 12.718 9496 Z= 0.346 Chirality : 0.045 0.199 1018 Planarity : 0.004 0.039 1217 Dihedral : 5.609 29.959 980 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 11.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.13 % Favored : 92.87 % Rotamer: Outliers : 1.91 % Allowed : 19.35 % Favored : 78.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: -3.12 (0.26), residues: 855 helix: -4.97 (0.30), residues: 27 sheet: -1.99 (0.26), residues: 355 loop : -1.91 (0.26), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP L 96 HIS 0.007 0.002 HIS L 38 PHE 0.021 0.002 PHE G 377 TYR 0.017 0.002 TYR C 32 ARG 0.002 0.000 ARG G 466 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1710 Ramachandran restraints generated. 855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1710 Ramachandran restraints generated. 855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 734 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 134 time to evaluate : 0.782 Fit side-chains outliers start: 14 outliers final: 10 residues processed: 142 average time/residue: 0.1812 time to fit residues: 34.8515 Evaluate side-chains 141 residues out of total 734 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 131 time to evaluate : 0.757 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.0645 time to fit residues: 2.2077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 72 optimal weight: 0.3980 chunk 15 optimal weight: 0.9990 chunk 47 optimal weight: 7.9990 chunk 19 optimal weight: 5.9990 chunk 80 optimal weight: 6.9990 chunk 66 optimal weight: 0.7980 chunk 37 optimal weight: 3.9990 chunk 6 optimal weight: 0.9990 chunk 26 optimal weight: 1.9990 chunk 42 optimal weight: 4.9990 chunk 77 optimal weight: 0.4980 overall best weight: 0.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 3 GLN D 38 GLN ** C 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 39 GLN C 82 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5870 moved from start: 0.2512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 6988 Z= 0.226 Angle : 0.592 10.550 9496 Z= 0.295 Chirality : 0.042 0.188 1018 Planarity : 0.004 0.041 1217 Dihedral : 5.248 27.954 980 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 10.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 1.36 % Allowed : 21.39 % Favored : 77.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.82 (0.27), residues: 855 helix: -4.80 (0.40), residues: 27 sheet: -1.79 (0.27), residues: 346 loop : -1.72 (0.26), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP G 436 HIS 0.006 0.001 HIS C 82 PHE 0.022 0.002 PHE G 456 TYR 0.016 0.001 TYR C 32 ARG 0.002 0.000 ARG A 63 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1710 Ramachandran restraints generated. 855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1710 Ramachandran restraints generated. 855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 734 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 132 time to evaluate : 0.823 Fit side-chains outliers start: 10 outliers final: 6 residues processed: 136 average time/residue: 0.1908 time to fit residues: 34.9995 Evaluate side-chains 136 residues out of total 734 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 130 time to evaluate : 0.823 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0738 time to fit residues: 1.9094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 9 optimal weight: 0.9980 chunk 45 optimal weight: 0.1980 chunk 58 optimal weight: 1.9990 chunk 67 optimal weight: 0.0770 chunk 44 optimal weight: 0.9980 chunk 79 optimal weight: 0.9990 chunk 50 optimal weight: 1.9990 chunk 48 optimal weight: 0.5980 chunk 36 optimal weight: 1.9990 chunk 49 optimal weight: 0.9990 chunk 31 optimal weight: 0.8980 overall best weight: 0.5538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 3 GLN D 42 ASN C 6 GLN C 82 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5851 moved from start: 0.2649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6988 Z= 0.196 Angle : 0.574 9.419 9496 Z= 0.283 Chirality : 0.042 0.204 1018 Planarity : 0.004 0.040 1217 Dihedral : 4.992 25.370 980 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 1.23 % Allowed : 21.53 % Favored : 77.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.50 (0.27), residues: 855 helix: -4.61 (0.55), residues: 26 sheet: -1.51 (0.26), residues: 364 loop : -1.53 (0.27), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP G 436 HIS 0.006 0.001 HIS C 82 PHE 0.027 0.001 PHE G 456 TYR 0.016 0.001 TYR C 32 ARG 0.002 0.000 ARG A 63 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1710 Ramachandran restraints generated. 855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1710 Ramachandran restraints generated. 855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 734 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 125 time to evaluate : 0.905 Fit side-chains outliers start: 9 outliers final: 7 residues processed: 125 average time/residue: 0.1923 time to fit residues: 32.5008 Evaluate side-chains 130 residues out of total 734 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 123 time to evaluate : 0.902 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1344 time to fit residues: 3.4039 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 47 optimal weight: 8.9990 chunk 24 optimal weight: 0.7980 chunk 15 optimal weight: 0.0000 chunk 50 optimal weight: 0.0020 chunk 54 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 62 optimal weight: 0.9980 chunk 72 optimal weight: 1.9990 chunk 76 optimal weight: 3.9990 chunk 69 optimal weight: 5.9990 overall best weight: 0.7594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 42 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5858 moved from start: 0.2751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 6988 Z= 0.237 Angle : 0.590 9.704 9496 Z= 0.292 Chirality : 0.042 0.209 1018 Planarity : 0.004 0.038 1217 Dihedral : 5.018 25.486 980 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 1.09 % Allowed : 21.66 % Favored : 77.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.37 (0.28), residues: 855 helix: -4.24 (0.73), residues: 20 sheet: -1.44 (0.26), residues: 369 loop : -1.50 (0.28), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP G 436 HIS 0.010 0.001 HIS C 82 PHE 0.015 0.002 PHE A 29 TYR 0.015 0.001 TYR C 32 ARG 0.002 0.000 ARG G 408 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1710 Ramachandran restraints generated. 855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1710 Ramachandran restraints generated. 855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 734 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 126 time to evaluate : 0.813 Fit side-chains outliers start: 8 outliers final: 5 residues processed: 128 average time/residue: 0.1838 time to fit residues: 31.8502 Evaluate side-chains 130 residues out of total 734 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 125 time to evaluate : 0.707 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0633 time to fit residues: 1.5415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 74 optimal weight: 0.3980 chunk 76 optimal weight: 3.9990 chunk 44 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 58 optimal weight: 4.9990 chunk 22 optimal weight: 0.0060 chunk 67 optimal weight: 0.9990 chunk 70 optimal weight: 0.6980 chunk 48 optimal weight: 0.9980 chunk 78 optimal weight: 3.9990 chunk 37 optimal weight: 1.9990 overall best weight: 0.6198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 42 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5850 moved from start: 0.2826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 6988 Z= 0.209 Angle : 0.571 8.983 9496 Z= 0.283 Chirality : 0.041 0.201 1018 Planarity : 0.004 0.037 1217 Dihedral : 4.910 25.227 980 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 0.95 % Allowed : 22.34 % Favored : 76.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.22 (0.28), residues: 855 helix: -4.02 (0.81), residues: 20 sheet: -1.35 (0.27), residues: 367 loop : -1.39 (0.28), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP G 436 HIS 0.010 0.001 HIS C 82 PHE 0.027 0.002 PHE G 456 TYR 0.016 0.001 TYR G 473 ARG 0.002 0.000 ARG G 408 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1710 Ramachandran restraints generated. 855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1710 Ramachandran restraints generated. 855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 734 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 127 time to evaluate : 0.798 Fit side-chains outliers start: 7 outliers final: 4 residues processed: 129 average time/residue: 0.1858 time to fit residues: 32.5365 Evaluate side-chains 129 residues out of total 734 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 125 time to evaluate : 0.797 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0754 time to fit residues: 1.6106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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-1.21rc1-5172/modules/cctbx_project/iotbx/cli_parser.py", line 931, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/programs/real_space_refine.py", line 191, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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-1.21rc1-5172/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-1.21rc1-5172/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-1.21rc1-5172/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-1.21rc1-5172/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-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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-1.21rc1-5172/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-1.21rc1-5172/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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-1.21rc1-5172/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-1.21rc1-5172/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-1.21rc1-5172/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-1.21rc1-5172/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: 67.8216 > 50: distance: 55 - 218: 38.414 distance: 58 - 230: 24.808 distance: 67 - 233: 31.335 distance: 114 - 211: 30.673 distance: 160 - 166: 14.578 distance: 166 - 167: 19.583 distance: 167 - 168: 10.411 distance: 167 - 170: 16.161 distance: 168 - 169: 20.797 distance: 168 - 177: 11.612 distance: 170 - 171: 12.913 distance: 171 - 172: 23.359 distance: 171 - 173: 10.797 distance: 172 - 174: 12.109 distance: 173 - 175: 7.934 distance: 174 - 176: 18.532 distance: 175 - 176: 25.050 distance: 177 - 178: 9.281 distance: 178 - 181: 11.074 distance: 179 - 180: 26.321 distance: 179 - 191: 25.480 distance: 181 - 182: 12.320 distance: 182 - 183: 7.252 distance: 183 - 185: 3.938 distance: 184 - 186: 4.427 distance: 184 - 187: 5.240 distance: 185 - 186: 4.936 distance: 187 - 189: 5.292 distance: 188 - 190: 6.431 distance: 189 - 190: 3.407 distance: 191 - 192: 35.595 distance: 192 - 193: 25.293 distance: 193 - 194: 31.037 distance: 193 - 195: 6.543 distance: 195 - 196: 19.802 distance: 196 - 197: 43.552 distance: 196 - 199: 11.960 distance: 197 - 198: 30.716 distance: 197 - 204: 37.738 distance: 199 - 200: 30.147 distance: 200 - 201: 35.473 distance: 201 - 202: 19.223 distance: 201 - 203: 24.206 distance: 204 - 205: 48.991 distance: 205 - 206: 42.458 distance: 206 - 207: 22.076 distance: 206 - 208: 20.740 distance: 208 - 209: 32.523 distance: 209 - 210: 13.026 distance: 209 - 212: 29.647 distance: 210 - 211: 18.462 distance: 210 - 215: 42.223 distance: 212 - 213: 41.059 distance: 212 - 214: 32.645 distance: 215 - 216: 15.782 distance: 216 - 217: 18.834 distance: 216 - 219: 15.322 distance: 217 - 218: 66.722 distance: 219 - 220: 20.108 distance: 219 - 221: 24.835 distance: 222 - 223: 7.805 distance: 223 - 224: 11.861 distance: 223 - 226: 19.089 distance: 224 - 225: 18.660 distance: 224 - 230: 21.739 distance: 226 - 227: 52.402 distance: 227 - 228: 31.768 distance: 227 - 229: 25.391 distance: 230 - 231: 23.660 distance: 231 - 232: 10.853 distance: 231 - 234: 7.511 distance: 232 - 233: 14.179 distance: 232 - 237: 9.782 distance: 234 - 235: 19.591 distance: 234 - 236: 9.600 distance: 237 - 238: 10.720 distance: 238 - 241: 5.425 distance: 239 - 240: 3.085 distance: 239 - 244: 11.178 distance: 241 - 242: 11.480 distance: 241 - 243: 14.712