Starting phenix.real_space_refine on Fri Dec 8 06:31:08 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ck6_30382/12_2023/7ck6_30382_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ck6_30382/12_2023/7ck6_30382.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ck6_30382/12_2023/7ck6_30382.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ck6_30382/12_2023/7ck6_30382.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ck6_30382/12_2023/7ck6_30382_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ck6_30382/12_2023/7ck6_30382_updated.pdb" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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 1 5.49 5 S 32 5.16 5 C 4808 2.51 5 N 1281 2.21 5 O 1338 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 85": "OE1" <-> "OE2" Residue "A ARG 88": "NH1" <-> "NH2" Residue "A GLU 244": "OE1" <-> "OE2" Residue "A PHE 314": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 85": "OE1" <-> "OE2" Residue "B ARG 88": "NH1" <-> "NH2" Residue "B GLU 244": "OE1" <-> "OE2" Residue "B PHE 314": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 82": "NH1" <-> "NH2" Residue "C GLU 109": "OE1" <-> "OE2" Residue "D ARG 82": "NH1" <-> "NH2" Residue "D GLU 109": "OE1" <-> "OE2" Residue "E ARG 38": "NH1" <-> "NH2" Residue "E ARG 42": "NH1" <-> "NH2" Residue "E ARG 60": "NH1" <-> "NH2" Residue "F ARG 38": "NH1" <-> "NH2" Residue "F ARG 42": "NH1" <-> "NH2" Residue "F ARG 43": "NH1" <-> "NH2" Residue "F ARG 60": "NH1" <-> "NH2" Residue "G ARG 38": "NH1" <-> "NH2" Residue "G GLU 46": "OE1" <-> "OE2" Residue "H GLU 46": "OE1" <-> "OE2" Residue "I GLU 15": "OE1" <-> "OE2" Residue "I ARG 39": "NH1" <-> "NH2" Residue "J GLU 15": "OE1" <-> "OE2" Residue "J ARG 39": "NH1" <-> "NH2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 7460 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 2179 Number of conformers: 1 Conformer: "" Number of residues, atoms: 284, 2179 Classifications: {'peptide': 284} Link IDs: {'PTRANS': 13, 'TRANS': 270} Chain: "B" Number of atoms: 2179 Number of conformers: 1 Conformer: "" Number of residues, atoms: 284, 2179 Classifications: {'peptide': 284} Link IDs: {'PTRANS': 13, 'TRANS': 270} Chain: "C" Number of atoms: 444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 444 Classifications: {'peptide': 53} Link IDs: {'PTRANS': 1, 'TRANS': 51} Chain: "D" Number of atoms: 444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 444 Classifications: {'peptide': 53} Link IDs: {'PTRANS': 1, 'TRANS': 51} Chain: "E" Number of atoms: 361 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 361 Classifications: {'peptide': 44} Link IDs: {'TRANS': 43} Chain: "F" Number of atoms: 361 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 361 Classifications: {'peptide': 44} Link IDs: {'TRANS': 43} Chain: "G" Number of atoms: 399 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 399 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 4, 'TRANS': 44} Chain: "H" Number of atoms: 399 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 399 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 4, 'TRANS': 44} Chain: "I" Number of atoms: 320 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 320 Classifications: {'peptide': 38} Link IDs: {'PTRANS': 2, 'TRANS': 35} Chain: "J" Number of atoms: 320 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 320 Classifications: {'peptide': 38} Link IDs: {'PTRANS': 2, 'TRANS': 35} Chain: "A" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 54 Unusual residues: {'PC1': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.42, per 1000 atoms: 0.59 Number of scatterers: 7460 At special positions: 0 Unit cell: (111.24, 145.8, 96.12, 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 32 16.00 P 1 15.00 O 1338 8.00 N 1281 7.00 C 4808 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: 2.87 Conformation dependent library (CDL) restraints added in 1.2 seconds 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1716 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 15 helices and 4 sheets defined 34.6% alpha, 31.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.29 Creating SS restraints... Processing helix chain 'A' and resid 84 through 91 removed outlier: 4.045A pdb=" N HIS A 87 " --> pdb=" O GLU A 84 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N LYS A 89 " --> pdb=" O CYS A 86 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N CYS A 90 " --> pdb=" O HIS A 87 " (cutoff:3.500A) Processing helix chain 'B' and resid 84 through 91 removed outlier: 4.045A pdb=" N HIS B 87 " --> pdb=" O GLU B 84 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N LYS B 89 " --> pdb=" O CYS B 86 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N CYS B 90 " --> pdb=" O HIS B 87 " (cutoff:3.500A) Processing helix chain 'C' and resid 67 through 117 Proline residue: C 98 - end of helix removed outlier: 3.784A pdb=" N GLU C 102 " --> pdb=" O PRO C 98 " (cutoff:3.500A) Processing helix chain 'D' and resid 67 through 95 Processing helix chain 'D' and resid 97 through 117 Processing helix chain 'E' and resid 24 through 34 Processing helix chain 'E' and resid 43 through 65 removed outlier: 3.509A pdb=" N GLY E 50 " --> pdb=" O ILE E 46 " (cutoff:3.500A) Processing helix chain 'F' and resid 24 through 34 Processing helix chain 'F' and resid 44 through 65 Processing helix chain 'G' and resid 7 through 36 removed outlier: 3.892A pdb=" N TRP G 25 " --> pdb=" O PHE G 21 " (cutoff:3.500A) removed outlier: 5.252A pdb=" N ILE G 28 " --> pdb=" O ARG G 24 " (cutoff:3.500A) Proline residue: G 29 - end of helix Processing helix chain 'G' and resid 49 through 53 removed outlier: 3.653A pdb=" N LEU G 53 " --> pdb=" O VAL G 49 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 49 through 53' Processing helix chain 'H' and resid 7 through 36 removed outlier: 3.893A pdb=" N TRP H 25 " --> pdb=" O PHE H 21 " (cutoff:3.500A) removed outlier: 5.252A pdb=" N ILE H 28 " --> pdb=" O ARG H 24 " (cutoff:3.500A) Proline residue: H 29 - end of helix Processing helix chain 'H' and resid 49 through 53 removed outlier: 3.653A pdb=" N LEU H 53 " --> pdb=" O VAL H 49 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 49 through 53' Processing helix chain 'I' and resid 13 through 47 Proline residue: I 42 - end of helix removed outlier: 3.793A pdb=" N LYS I 47 " --> pdb=" O PHE I 43 " (cutoff:3.500A) Processing helix chain 'J' and resid 13 through 47 Proline residue: J 42 - end of helix removed outlier: 3.793A pdb=" N LYS J 47 " --> pdb=" O PHE J 43 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 103 through 107 removed outlier: 3.671A pdb=" N PHE A 301 " --> pdb=" O VAL A 318 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N ILE A 323 " --> pdb=" O ASP A 319 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N LEU A 337 " --> pdb=" O LEU A 332 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 344 through 346 removed outlier: 3.731A pdb=" N LYS A 351 " --> pdb=" O ASN A 346 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 103 through 107 removed outlier: 3.670A pdb=" N PHE B 301 " --> pdb=" O VAL B 318 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N ILE B 323 " --> pdb=" O ASP B 319 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N LEU B 337 " --> pdb=" O LEU B 332 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 344 through 346 removed outlier: 3.669A pdb=" N LYS B 351 " --> pdb=" O ASN B 346 " (cutoff:3.500A) 499 hydrogen bonds defined for protein. 1419 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: 2.32 Time building geometry restraints manager: 3.11 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 2343 1.33 - 1.45: 1063 1.45 - 1.57: 4157 1.57 - 1.69: 2 1.69 - 1.80: 56 Bond restraints: 7621 Sorted by residual: bond pdb=" C31 PC1 A 401 " pdb=" O31 PC1 A 401 " ideal model delta sigma weight residual 1.330 1.455 -0.125 2.00e-02 2.50e+03 3.88e+01 bond pdb=" C21 PC1 A 401 " pdb=" O21 PC1 A 401 " ideal model delta sigma weight residual 1.331 1.454 -0.123 2.00e-02 2.50e+03 3.76e+01 bond pdb=" CA HIS A 347 " pdb=" C HIS A 347 " ideal model delta sigma weight residual 1.523 1.473 0.050 1.34e-02 5.57e+03 1.42e+01 bond pdb=" CA PRO A 333 " pdb=" C PRO A 333 " ideal model delta sigma weight residual 1.517 1.551 -0.034 9.30e-03 1.16e+04 1.33e+01 bond pdb=" CA PRO B 333 " pdb=" C PRO B 333 " ideal model delta sigma weight residual 1.517 1.551 -0.034 9.30e-03 1.16e+04 1.32e+01 ... (remaining 7616 not shown) Histogram of bond angle deviations from ideal: 99.58 - 106.47: 210 106.47 - 113.36: 4152 113.36 - 120.25: 2742 120.25 - 127.14: 3105 127.14 - 134.03: 90 Bond angle restraints: 10299 Sorted by residual: angle pdb=" N PRO A 333 " pdb=" CA PRO A 333 " pdb=" C PRO A 333 " ideal model delta sigma weight residual 110.70 124.06 -13.36 1.22e+00 6.72e-01 1.20e+02 angle pdb=" N PRO B 333 " pdb=" CA PRO B 333 " pdb=" C PRO B 333 " ideal model delta sigma weight residual 110.70 124.05 -13.35 1.22e+00 6.72e-01 1.20e+02 angle pdb=" C GLU H 46 " pdb=" N PRO H 47 " pdb=" CA PRO H 47 " ideal model delta sigma weight residual 119.84 132.57 -12.73 1.25e+00 6.40e-01 1.04e+02 angle pdb=" C GLU G 46 " pdb=" N PRO G 47 " pdb=" CA PRO G 47 " ideal model delta sigma weight residual 119.84 132.41 -12.57 1.25e+00 6.40e-01 1.01e+02 angle pdb=" N THR B 292 " pdb=" CA THR B 292 " pdb=" C THR B 292 " ideal model delta sigma weight residual 111.14 119.93 -8.79 1.08e+00 8.57e-01 6.62e+01 ... (remaining 10294 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.13: 3951 15.13 - 30.26: 468 30.26 - 45.39: 82 45.39 - 60.51: 24 60.51 - 75.64: 7 Dihedral angle restraints: 4532 sinusoidal: 1864 harmonic: 2668 Sorted by residual: dihedral pdb=" N GLN B 182 " pdb=" C GLN B 182 " pdb=" CA GLN B 182 " pdb=" CB GLN B 182 " ideal model delta harmonic sigma weight residual 122.80 134.15 -11.35 0 2.50e+00 1.60e-01 2.06e+01 dihedral pdb=" N GLN A 182 " pdb=" C GLN A 182 " pdb=" CA GLN A 182 " pdb=" CB GLN A 182 " ideal model delta harmonic sigma weight residual 122.80 134.05 -11.25 0 2.50e+00 1.60e-01 2.02e+01 dihedral pdb=" C GLN B 182 " pdb=" N GLN B 182 " pdb=" CA GLN B 182 " pdb=" CB GLN B 182 " ideal model delta harmonic sigma weight residual -122.60 -133.46 10.86 0 2.50e+00 1.60e-01 1.89e+01 ... (remaining 4529 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.096: 1029 0.096 - 0.192: 96 0.192 - 0.288: 13 0.288 - 0.384: 3 0.384 - 0.480: 2 Chirality restraints: 1143 Sorted by residual: chirality pdb=" CA GLN B 182 " pdb=" N GLN B 182 " pdb=" C GLN B 182 " pdb=" CB GLN B 182 " both_signs ideal model delta sigma weight residual False 2.51 2.03 0.48 2.00e-01 2.50e+01 5.76e+00 chirality pdb=" CA GLN A 182 " pdb=" N GLN A 182 " pdb=" C GLN A 182 " pdb=" CB GLN A 182 " both_signs ideal model delta sigma weight residual False 2.51 2.04 0.48 2.00e-01 2.50e+01 5.65e+00 chirality pdb=" CA PRO A 333 " pdb=" N PRO A 333 " pdb=" C PRO A 333 " pdb=" CB PRO A 333 " both_signs ideal model delta sigma weight residual False 2.72 2.38 0.34 2.00e-01 2.50e+01 2.81e+00 ... (remaining 1140 not shown) Planarity restraints: 1310 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU H 46 " -0.044 5.00e-02 4.00e+02 6.54e-02 6.84e+00 pdb=" N PRO H 47 " 0.113 5.00e-02 4.00e+02 pdb=" CA PRO H 47 " -0.039 5.00e-02 4.00e+02 pdb=" CD PRO H 47 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU G 46 " 0.044 5.00e-02 4.00e+02 6.54e-02 6.84e+00 pdb=" N PRO G 47 " -0.113 5.00e-02 4.00e+02 pdb=" CA PRO G 47 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO G 47 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA THR C 66 " -0.012 2.00e-02 2.50e+03 2.53e-02 6.38e+00 pdb=" C THR C 66 " 0.044 2.00e-02 2.50e+03 pdb=" O THR C 66 " -0.017 2.00e-02 2.50e+03 pdb=" N PHE C 67 " -0.015 2.00e-02 2.50e+03 ... (remaining 1307 not shown) Histogram of nonbonded interaction distances: 1.65 - 2.30: 29 2.30 - 2.95: 3719 2.95 - 3.60: 10420 3.60 - 4.25: 14270 4.25 - 4.90: 25387 Nonbonded interactions: 53825 Sorted by model distance: nonbonded pdb=" O ASN F 39 " pdb=" CE2 PHE F 41 " model vdw 1.652 3.340 nonbonded pdb=" O LEU H 30 " pdb=" CD2 LEU H 34 " model vdw 1.677 3.460 nonbonded pdb=" O ASP F 37 " pdb=" OD1 ASP F 40 " model vdw 1.722 3.040 nonbonded pdb=" OG1 THR B 297 " pdb=" ND2 ASN F 48 " model vdw 1.824 2.520 nonbonded pdb=" O LEU G 30 " pdb=" CD2 LEU G 34 " model vdw 1.843 3.460 ... (remaining 53820 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 77 through 360) selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' } ncs_group { reference = chain 'I' selection = chain 'J' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 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: 1.040 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: 3.750 Check model and map are aligned: 0.110 Set scattering table: 0.080 Process input model: 23.270 Find NCS groups from input model: 0.400 Set up NCS constraints: 0.050 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:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7424 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 : 0.008 0.125 7621 Z= 0.508 Angle : 1.142 13.363 10299 Z= 0.740 Chirality : 0.065 0.480 1143 Planarity : 0.005 0.065 1310 Dihedral : 13.465 75.643 2816 Min Nonbonded Distance : 1.652 Molprobity Statistics. All-atom Clashscore : 36.32 Ramachandran Plot: Outliers : 0.76 % Allowed : 6.11 % Favored : 93.12 % Rotamer: Outliers : 4.12 % Allowed : 12.38 % Favored : 83.50 % Cbeta Deviations : 0.23 % 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: 0.38 (0.28), residues: 916 helix: 2.24 (0.30), residues: 300 sheet: 0.39 (0.27), residues: 378 loop : -2.66 (0.34), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 86 HIS 0.003 0.001 HIS A 220 PHE 0.031 0.002 PHE A 344 TYR 0.018 0.002 TYR A 129 ARG 0.004 0.000 ARG I 21 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 305 time to evaluate : 0.792 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 33 outliers final: 12 residues processed: 319 average time/residue: 0.3046 time to fit residues: 117.4980 Evaluate side-chains 176 residues out of total 800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 164 time to evaluate : 0.954 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.0767 time to fit residues: 2.8336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 74 optimal weight: 0.0770 chunk 66 optimal weight: 10.0000 chunk 37 optimal weight: 6.9990 chunk 22 optimal weight: 3.9990 chunk 44 optimal weight: 0.6980 chunk 35 optimal weight: 5.9990 chunk 68 optimal weight: 0.7980 chunk 26 optimal weight: 2.9990 chunk 41 optimal weight: 8.9990 chunk 51 optimal weight: 3.9990 chunk 79 optimal weight: 2.9990 overall best weight: 1.5142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 114 GLN ** A 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 220 HIS A 223 GLN ** A 238 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 114 GLN ** B 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 220 HIS B 223 GLN ** B 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 110 GLN E 23 ASN E 48 ASN E 61 ASN ** F 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 48 ASN F 61 ASN G 10 GLN H 10 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7527 moved from start: 0.4792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 7621 Z= 0.254 Angle : 0.897 12.014 10299 Z= 0.436 Chirality : 0.049 0.369 1143 Planarity : 0.006 0.056 1310 Dihedral : 6.764 53.398 1046 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 17.06 Ramachandran Plot: Outliers : 0.22 % Allowed : 5.02 % Favored : 94.76 % Rotamer: Outliers : 4.75 % Allowed : 21.00 % Favored : 74.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.26 (0.29), residues: 916 helix: 3.04 (0.28), residues: 292 sheet: 1.09 (0.26), residues: 376 loop : -2.51 (0.38), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP G 54 HIS 0.005 0.001 HIS A 112 PHE 0.026 0.002 PHE C 101 TYR 0.029 0.002 TYR I 34 ARG 0.006 0.001 ARG C 79 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 197 time to evaluate : 0.956 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 38 outliers final: 14 residues processed: 217 average time/residue: 0.2002 time to fit residues: 57.7052 Evaluate side-chains 177 residues out of total 800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 163 time to evaluate : 0.952 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.0703 time to fit residues: 2.9090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 44 optimal weight: 7.9990 chunk 24 optimal weight: 2.9990 chunk 66 optimal weight: 9.9990 chunk 54 optimal weight: 3.9990 chunk 22 optimal weight: 3.9990 chunk 80 optimal weight: 6.9990 chunk 86 optimal weight: 1.9990 chunk 71 optimal weight: 3.9990 chunk 79 optimal weight: 8.9990 chunk 27 optimal weight: 0.9990 chunk 64 optimal weight: 3.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 238 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 97 GLN B 140 GLN B 353 GLN ** F 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 48 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7601 moved from start: 0.5507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 7621 Z= 0.276 Angle : 0.843 11.259 10299 Z= 0.409 Chirality : 0.048 0.248 1143 Planarity : 0.005 0.046 1310 Dihedral : 6.894 58.757 1046 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 17.06 Ramachandran Plot: Outliers : 0.22 % Allowed : 6.22 % Favored : 93.56 % Rotamer: Outliers : 4.12 % Allowed : 23.50 % Favored : 72.38 % 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: 1.19 (0.28), residues: 916 helix: 2.85 (0.29), residues: 300 sheet: 0.93 (0.25), residues: 378 loop : -2.31 (0.40), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP G 54 HIS 0.005 0.001 HIS B 238 PHE 0.033 0.002 PHE C 101 TYR 0.032 0.002 TYR J 34 ARG 0.005 0.001 ARG A 173 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 171 time to evaluate : 0.943 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 33 outliers final: 16 residues processed: 189 average time/residue: 0.1912 time to fit residues: 48.3302 Evaluate side-chains 161 residues out of total 800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 145 time to evaluate : 0.854 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.0701 time to fit residues: 3.1824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 79 optimal weight: 9.9990 chunk 60 optimal weight: 7.9990 chunk 41 optimal weight: 0.4980 chunk 8 optimal weight: 8.9990 chunk 38 optimal weight: 9.9990 chunk 53 optimal weight: 0.9980 chunk 80 optimal weight: 2.9990 chunk 85 optimal weight: 3.9990 chunk 76 optimal weight: 0.8980 chunk 22 optimal weight: 9.9990 chunk 70 optimal weight: 0.2980 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 97 GLN ** A 238 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 353 GLN ** B 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 116 GLN ** F 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7567 moved from start: 0.6055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 7621 Z= 0.220 Angle : 0.896 13.660 10299 Z= 0.412 Chirality : 0.048 0.350 1143 Planarity : 0.005 0.045 1310 Dihedral : 6.729 59.035 1046 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 16.66 Ramachandran Plot: Outliers : 0.22 % Allowed : 5.46 % Favored : 94.32 % Rotamer: Outliers : 2.12 % Allowed : 25.00 % Favored : 72.88 % 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: 1.21 (0.28), residues: 916 helix: 2.77 (0.29), residues: 300 sheet: 1.02 (0.25), residues: 376 loop : -2.30 (0.38), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP G 54 HIS 0.005 0.001 HIS B 238 PHE 0.047 0.002 PHE C 101 TYR 0.015 0.001 TYR J 34 ARG 0.009 0.001 ARG A 293 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 168 time to evaluate : 0.841 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 17 outliers final: 10 residues processed: 173 average time/residue: 0.1946 time to fit residues: 44.8171 Evaluate side-chains 160 residues out of total 800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 150 time to evaluate : 0.871 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.0709 time to fit residues: 2.4528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 48 optimal weight: 6.9990 chunk 1 optimal weight: 1.9990 chunk 63 optimal weight: 2.9990 chunk 35 optimal weight: 10.0000 chunk 72 optimal weight: 0.8980 chunk 58 optimal weight: 0.9990 chunk 0 optimal weight: 9.9990 chunk 43 optimal weight: 10.0000 chunk 76 optimal weight: 0.0980 chunk 21 optimal weight: 9.9990 chunk 28 optimal weight: 8.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 113 GLN ** F 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7582 moved from start: 0.6336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 7621 Z= 0.214 Angle : 0.892 13.558 10299 Z= 0.407 Chirality : 0.048 0.358 1143 Planarity : 0.005 0.057 1310 Dihedral : 6.756 58.909 1046 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 14.26 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.57 % Favored : 94.32 % Rotamer: Outliers : 1.50 % Allowed : 27.75 % Favored : 70.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.21 (0.28), residues: 916 helix: 2.67 (0.29), residues: 300 sheet: 1.03 (0.26), residues: 376 loop : -2.17 (0.39), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP G 54 HIS 0.005 0.001 HIS B 238 PHE 0.039 0.002 PHE C 101 TYR 0.013 0.001 TYR J 34 ARG 0.006 0.001 ARG J 29 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 159 time to evaluate : 0.897 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 6 residues processed: 164 average time/residue: 0.2052 time to fit residues: 44.4741 Evaluate side-chains 155 residues out of total 800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 149 time to evaluate : 0.898 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0722 time to fit residues: 1.8928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 76 optimal weight: 2.9990 chunk 16 optimal weight: 9.9990 chunk 49 optimal weight: 9.9990 chunk 20 optimal weight: 7.9990 chunk 85 optimal weight: 3.9990 chunk 70 optimal weight: 0.8980 chunk 39 optimal weight: 0.2980 chunk 7 optimal weight: 5.9990 chunk 28 optimal weight: 8.9990 chunk 44 optimal weight: 1.9990 chunk 82 optimal weight: 0.0870 overall best weight: 1.2562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 48 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7576 moved from start: 0.6587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 7621 Z= 0.213 Angle : 0.913 15.158 10299 Z= 0.413 Chirality : 0.049 0.393 1143 Planarity : 0.005 0.048 1310 Dihedral : 6.754 59.480 1046 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 14.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Rotamer: Outliers : 1.88 % Allowed : 28.25 % Favored : 69.88 % 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: 1.20 (0.29), residues: 916 helix: 2.50 (0.30), residues: 300 sheet: 1.08 (0.26), residues: 378 loop : -2.04 (0.40), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 57 HIS 0.004 0.001 HIS B 238 PHE 0.020 0.001 PHE E 41 TYR 0.022 0.001 TYR J 34 ARG 0.010 0.001 ARG J 29 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 161 time to evaluate : 0.884 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 15 outliers final: 9 residues processed: 166 average time/residue: 0.1938 time to fit residues: 42.9313 Evaluate side-chains 161 residues out of total 800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 152 time to evaluate : 0.767 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.0664 time to fit residues: 2.1727 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 9 optimal weight: 20.0000 chunk 48 optimal weight: 4.9990 chunk 62 optimal weight: 2.9990 chunk 71 optimal weight: 8.9990 chunk 47 optimal weight: 9.9990 chunk 84 optimal weight: 6.9990 chunk 53 optimal weight: 5.9990 chunk 51 optimal weight: 5.9990 chunk 39 optimal weight: 5.9990 chunk 52 optimal weight: 4.9990 chunk 33 optimal weight: 6.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 238 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 30 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7709 moved from start: 0.6868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 7621 Z= 0.403 Angle : 0.974 14.058 10299 Z= 0.461 Chirality : 0.050 0.351 1143 Planarity : 0.005 0.050 1310 Dihedral : 7.404 58.258 1046 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 20.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.22 % Favored : 93.78 % Rotamer: Outliers : 1.50 % Allowed : 29.00 % Favored : 69.50 % 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: 0.80 (0.29), residues: 916 helix: 2.01 (0.29), residues: 310 sheet: 0.92 (0.26), residues: 380 loop : -2.37 (0.42), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP E 57 HIS 0.005 0.002 HIS A 166 PHE 0.021 0.002 PHE E 41 TYR 0.019 0.002 TYR B 275 ARG 0.009 0.001 ARG I 29 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 154 time to evaluate : 0.893 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 9 residues processed: 158 average time/residue: 0.2037 time to fit residues: 42.9911 Evaluate side-chains 155 residues out of total 800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 146 time to evaluate : 0.893 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.0773 time to fit residues: 2.4354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 50 optimal weight: 6.9990 chunk 25 optimal weight: 0.2980 chunk 16 optimal weight: 6.9990 chunk 53 optimal weight: 0.9980 chunk 57 optimal weight: 2.9990 chunk 41 optimal weight: 0.0060 chunk 7 optimal weight: 0.9990 chunk 66 optimal weight: 9.9990 chunk 77 optimal weight: 3.9990 chunk 81 optimal weight: 0.5980 chunk 74 optimal weight: 5.9990 overall best weight: 0.5798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 140 GLN ** A 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 39 ASN F 48 ASN J 30 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7611 moved from start: 0.6992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7621 Z= 0.209 Angle : 0.973 15.595 10299 Z= 0.440 Chirality : 0.050 0.402 1143 Planarity : 0.005 0.045 1310 Dihedral : 6.986 58.708 1046 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 15.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Rotamer: Outliers : 0.88 % Allowed : 30.12 % Favored : 69.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.99 (0.29), residues: 916 helix: 2.25 (0.30), residues: 304 sheet: 1.05 (0.27), residues: 378 loop : -2.29 (0.41), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP G 54 HIS 0.014 0.001 HIS B 130 PHE 0.024 0.002 PHE E 41 TYR 0.019 0.001 TYR J 34 ARG 0.003 0.000 ARG B 173 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 163 time to evaluate : 0.911 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 4 residues processed: 165 average time/residue: 0.2123 time to fit residues: 46.8963 Evaluate side-chains 155 residues out of total 800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 151 time to evaluate : 1.023 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0806 time to fit residues: 2.1093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- 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: 64.5519 > 50: distance: 32 - 57: 15.800 distance: 36 - 61: 24.305 distance: 52 - 57: 19.073 distance: 57 - 58: 10.113 distance: 58 - 59: 36.523 distance: 59 - 60: 47.583 distance: 59 - 61: 49.168 distance: 61 - 62: 33.942 distance: 62 - 63: 24.146 distance: 62 - 65: 20.928 distance: 63 - 64: 32.780 distance: 63 - 72: 28.882 distance: 65 - 66: 14.195 distance: 66 - 67: 39.729 distance: 66 - 68: 36.960 distance: 67 - 69: 39.361 distance: 68 - 70: 39.754 distance: 69 - 71: 12.598 distance: 70 - 71: 29.820 distance: 72 - 73: 24.126 distance: 73 - 74: 42.916 distance: 73 - 76: 32.150 distance: 74 - 75: 21.950 distance: 74 - 81: 37.581 distance: 76 - 77: 35.467 distance: 77 - 78: 31.939 distance: 78 - 79: 33.395 distance: 79 - 80: 12.209 distance: 81 - 82: 18.981 distance: 82 - 83: 17.538 distance: 82 - 85: 41.169 distance: 83 - 84: 41.181 distance: 83 - 92: 53.919 distance: 85 - 86: 37.316 distance: 86 - 87: 34.793 distance: 87 - 88: 30.247 distance: 88 - 89: 14.209 distance: 89 - 90: 21.351 distance: 89 - 91: 3.775 distance: 92 - 93: 41.840 distance: 93 - 94: 20.273 distance: 94 - 95: 20.251 distance: 94 - 96: 31.887 distance: 96 - 97: 24.202 distance: 97 - 98: 17.952 distance: 97 - 100: 8.474 distance: 98 - 99: 21.895 distance: 98 - 101: 40.086 distance: 101 - 102: 26.961 distance: 102 - 103: 32.549 distance: 102 - 105: 21.488 distance: 103 - 104: 27.765 distance: 103 - 109: 22.529 distance: 105 - 106: 12.555 distance: 106 - 107: 23.720 distance: 106 - 108: 22.471 distance: 109 - 110: 36.882 distance: 109 - 115: 42.720 distance: 110 - 111: 33.664 distance: 110 - 113: 43.775 distance: 111 - 112: 38.311 distance: 111 - 116: 54.678 distance: 113 - 114: 11.411 distance: 114 - 115: 47.839 distance: 116 - 117: 58.893 distance: 117 - 118: 54.547 distance: 118 - 119: 28.127 distance: 118 - 120: 13.719 distance: 120 - 121: 50.006 distance: 121 - 122: 16.631 distance: 121 - 124: 39.339 distance: 122 - 123: 18.722 distance: 122 - 128: 31.670 distance: 124 - 125: 28.941 distance: 125 - 126: 22.549 distance: 126 - 127: 28.995