Starting phenix.real_space_refine on Thu Nov 14 00:16:40 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9bhb_44539/11_2024/9bhb_44539.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9bhb_44539/11_2024/9bhb_44539.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9bhb_44539/11_2024/9bhb_44539.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9bhb_44539/11_2024/9bhb_44539.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9bhb_44539/11_2024/9bhb_44539.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9bhb_44539/11_2024/9bhb_44539.cif" } resolution = 3.1 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= 0.009 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 10 5.16 5 C 1681 2.51 5 N 441 2.21 5 O 494 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 2626 Number of models: 1 Model: "" Number of chains: 3 Chain: "H" Number of atoms: 931 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 931 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 3, 'TRANS': 115} Chain: "K" Number of atoms: 841 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 841 Classifications: {'peptide': 111} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 103} Chain: "A" Number of atoms: 854 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 854 Classifications: {'peptide': 98} Link IDs: {'TRANS': 97} Chain breaks: 3 Time building chain proxies: 3.28, per 1000 atoms: 1.25 Number of scatterers: 2626 At special positions: 0 Unit cell: (55.1, 64.525, 91.35, 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 10 16.00 O 494 8.00 N 441 7.00 C 1681 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 88 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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: 0.58 Conformation dependent library (CDL) restraints added in 389.4 milliseconds 632 Ramachandran restraints generated. 316 Oldfield, 0 Emsley, 316 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 612 Finding SS restraints... Secondary structure from input PDB file: 8 helices and 7 sheets defined 29.9% alpha, 27.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.37 Creating SS restraints... Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.516A pdb=" N PHE H 32 " --> pdb=" O PHE H 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 83 through 87 removed outlier: 3.781A pdb=" N ASP H 86 " --> pdb=" O ARG H 83 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N THR H 87 " --> pdb=" O ASP H 84 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 83 through 87' Processing helix chain 'K' and resid 79 through 83 removed outlier: 3.964A pdb=" N PHE K 83 " --> pdb=" O SER K 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 580 through 600 Processing helix chain 'A' and resid 622 through 640 removed outlier: 3.771A pdb=" N LYS A 638 " --> pdb=" O ASN A 634 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N VAL A 639 " --> pdb=" O GLU A 635 " (cutoff:3.500A) Processing helix chain 'A' and resid 664 through 672 removed outlier: 4.278A pdb=" N GLU A 671 " --> pdb=" O HIS A 667 " (cutoff:3.500A) Processing helix chain 'A' and resid 674 through 693 removed outlier: 3.777A pdb=" N TRP A 678 " --> pdb=" O LYS A 674 " (cutoff:3.500A) Processing helix chain 'A' and resid 704 through 717 Processing sheet with id=AA1, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AA2, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.560A pdb=" N ALA H 10 " --> pdb=" O LEU H 108 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N SER H 110 " --> pdb=" O ALA H 10 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N MET H 34 " --> pdb=" O TYR H 50 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N TYR H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ALA H 40 " --> pdb=" O GLY H 44 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N GLY H 44 " --> pdb=" O ALA H 40 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.560A pdb=" N ALA H 10 " --> pdb=" O LEU H 108 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N SER H 110 " --> pdb=" O ALA H 10 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N CYS H 92 " --> pdb=" O TRP H 103 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N TRP H 103 " --> pdb=" O CYS H 92 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N ARG H 94 " --> pdb=" O ASP H 101 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 17 through 20 removed outlier: 3.540A pdb=" N LEU H 80 " --> pdb=" O LEU H 20 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'K' and resid 4 through 5 Processing sheet with id=AA6, first strand: chain 'K' and resid 10 through 12 removed outlier: 5.869A pdb=" N LEU K 11 " --> pdb=" O GLU K 105 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ILE K 48 " --> pdb=" O TRP K 35 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N GLN K 37 " --> pdb=" O LEU K 46 " (cutoff:3.500A) removed outlier: 5.933A pdb=" N LEU K 46 " --> pdb=" O GLN K 37 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'K' and resid 19 through 20 113 hydrogen bonds defined for protein. 297 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.69 Time building geometry restraints manager: 0.68 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 812 1.34 - 1.46: 562 1.46 - 1.57: 1300 1.57 - 1.69: 0 1.69 - 1.81: 14 Bond restraints: 2688 Sorted by residual: bond pdb=" N SER K 7 " pdb=" CA SER K 7 " ideal model delta sigma weight residual 1.461 1.489 -0.028 9.20e-03 1.18e+04 9.51e+00 bond pdb=" N VAL K 3 " pdb=" CA VAL K 3 " ideal model delta sigma weight residual 1.458 1.494 -0.036 1.27e-02 6.20e+03 8.23e+00 bond pdb=" N GLU K 17 " pdb=" CA GLU K 17 " ideal model delta sigma weight residual 1.454 1.487 -0.032 1.16e-02 7.43e+03 7.79e+00 bond pdb=" N LEU K 13 " pdb=" CA LEU K 13 " ideal model delta sigma weight residual 1.454 1.488 -0.033 1.27e-02 6.20e+03 6.85e+00 bond pdb=" N ASP K 18 " pdb=" CA ASP K 18 " ideal model delta sigma weight residual 1.455 1.490 -0.034 1.33e-02 5.65e+03 6.59e+00 ... (remaining 2683 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.42: 3365 1.42 - 2.84: 217 2.84 - 4.25: 35 4.25 - 5.67: 9 5.67 - 7.09: 4 Bond angle restraints: 3630 Sorted by residual: angle pdb=" N ILE H 53 " pdb=" CA ILE H 53 " pdb=" C ILE H 53 " ideal model delta sigma weight residual 109.34 102.25 7.09 2.08e+00 2.31e-01 1.16e+01 angle pdb=" C ASP K 50 " pdb=" N ALA K 51 " pdb=" CA ALA K 51 " ideal model delta sigma weight residual 121.54 127.71 -6.17 1.91e+00 2.74e-01 1.04e+01 angle pdb=" CA THR K 5 " pdb=" CB THR K 5 " pdb=" OG1 THR K 5 " ideal model delta sigma weight residual 109.60 105.02 4.58 1.50e+00 4.44e-01 9.33e+00 angle pdb=" CG MET A 669 " pdb=" SD MET A 669 " pdb=" CE MET A 669 " ideal model delta sigma weight residual 100.90 94.18 6.72 2.20e+00 2.07e-01 9.32e+00 angle pdb=" CA GLN K 6 " pdb=" C GLN K 6 " pdb=" O GLN K 6 " ideal model delta sigma weight residual 121.58 118.25 3.33 1.12e+00 7.97e-01 8.84e+00 ... (remaining 3625 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.67: 1407 15.67 - 31.33: 128 31.33 - 46.99: 38 46.99 - 62.66: 6 62.66 - 78.32: 3 Dihedral angle restraints: 1582 sinusoidal: 634 harmonic: 948 Sorted by residual: dihedral pdb=" CA MET A 669 " pdb=" C MET A 669 " pdb=" N LYS A 670 " pdb=" CA LYS A 670 " ideal model delta harmonic sigma weight residual 180.00 156.54 23.46 0 5.00e+00 4.00e-02 2.20e+01 dihedral pdb=" CA LEU A 657 " pdb=" C LEU A 657 " pdb=" N ASN A 658 " pdb=" CA ASN A 658 " ideal model delta harmonic sigma weight residual 180.00 -160.90 -19.10 0 5.00e+00 4.00e-02 1.46e+01 dihedral pdb=" CB MET H 34 " pdb=" CG MET H 34 " pdb=" SD MET H 34 " pdb=" CE MET H 34 " ideal model delta sinusoidal sigma weight residual 60.00 119.06 -59.06 3 1.50e+01 4.44e-03 9.48e+00 ... (remaining 1579 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 256 0.044 - 0.089: 94 0.089 - 0.133: 27 0.133 - 0.177: 8 0.177 - 0.222: 3 Chirality restraints: 388 Sorted by residual: chirality pdb=" CA ILE H 53 " pdb=" N ILE H 53 " pdb=" C ILE H 53 " pdb=" CB ILE H 53 " both_signs ideal model delta sigma weight residual False 2.43 2.65 -0.22 2.00e-01 2.50e+01 1.23e+00 chirality pdb=" CA ILE K 48 " pdb=" N ILE K 48 " pdb=" C ILE K 48 " pdb=" CB ILE K 48 " both_signs ideal model delta sigma weight residual False 2.43 2.63 -0.19 2.00e-01 2.50e+01 9.29e-01 chirality pdb=" CA ILE K 2 " pdb=" N ILE K 2 " pdb=" C ILE K 2 " pdb=" CB ILE K 2 " both_signs ideal model delta sigma weight residual False 2.43 2.62 -0.19 2.00e-01 2.50e+01 8.59e-01 ... (remaining 385 not shown) Planarity restraints: 456 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE H 67 " -0.001 2.00e-02 2.50e+03 1.97e-02 6.82e+00 pdb=" CG PHE H 67 " 0.032 2.00e-02 2.50e+03 pdb=" CD1 PHE H 67 " -0.034 2.00e-02 2.50e+03 pdb=" CD2 PHE H 67 " -0.013 2.00e-02 2.50e+03 pdb=" CE1 PHE H 67 " 0.019 2.00e-02 2.50e+03 pdb=" CE2 PHE H 67 " -0.002 2.00e-02 2.50e+03 pdb=" CZ PHE H 67 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP K 96 " -0.010 2.00e-02 2.50e+03 1.08e-02 2.90e+00 pdb=" CG TRP K 96 " -0.014 2.00e-02 2.50e+03 pdb=" CD1 TRP K 96 " 0.023 2.00e-02 2.50e+03 pdb=" CD2 TRP K 96 " 0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP K 96 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP K 96 " -0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP K 96 " 0.012 2.00e-02 2.50e+03 pdb=" CZ2 TRP K 96 " -0.011 2.00e-02 2.50e+03 pdb=" CZ3 TRP K 96 " 0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP K 96 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU H 96 " -0.027 5.00e-02 4.00e+02 4.16e-02 2.76e+00 pdb=" N PRO H 97 " 0.072 5.00e-02 4.00e+02 pdb=" CA PRO H 97 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO H 97 " -0.023 5.00e-02 4.00e+02 ... (remaining 453 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 671 2.80 - 3.32: 2173 3.32 - 3.85: 4469 3.85 - 4.37: 5120 4.37 - 4.90: 9233 Nonbonded interactions: 21666 Sorted by model distance: nonbonded pdb=" OE1 GLU H 33 " pdb=" OH TYR H 50 " model vdw 2.274 3.040 nonbonded pdb=" O TYR K 49 " pdb=" OH TYR K 91 " model vdw 2.304 3.040 nonbonded pdb=" O ASP K 82 " pdb=" OH TYR K 86 " model vdw 2.332 3.040 nonbonded pdb=" OH TYR H 99 " pdb=" OE2 GLU A 675 " model vdw 2.363 3.040 nonbonded pdb=" NH1 ARG K 54 " pdb=" O ILE K 58 " model vdw 2.380 3.120 ... (remaining 21661 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 2.360 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: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 12.740 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 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:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 2688 Z= 0.388 Angle : 0.815 7.089 3630 Z= 0.480 Chirality : 0.054 0.222 388 Planarity : 0.006 0.042 456 Dihedral : 13.801 78.321 964 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.65 % Favored : 93.35 % Rotamer: Outliers : 0.35 % Allowed : 1.41 % Favored : 98.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -2.11 (0.45), residues: 316 helix: -1.44 (0.45), residues: 77 sheet: -1.17 (0.59), residues: 92 loop : -1.39 (0.49), residues: 147 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.003 TRP K 96 HIS 0.004 0.001 HIS A 667 PHE 0.034 0.003 PHE H 67 TYR 0.010 0.002 TYR K 49 ARG 0.005 0.001 ARG K 61 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 632 Ramachandran restraints generated. 316 Oldfield, 0 Emsley, 316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 632 Ramachandran restraints generated. 316 Oldfield, 0 Emsley, 316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 43 time to evaluate : 0.274 Fit side-chains REVERT: H 83 ARG cc_start: 0.7425 (mtt180) cc_final: 0.6945 (mtt-85) REVERT: K 100 GLN cc_start: 0.8370 (mp10) cc_final: 0.8087 (mp10) REVERT: A 680 LYS cc_start: 0.8178 (mtpt) cc_final: 0.7557 (mmmt) REVERT: A 706 LYS cc_start: 0.7845 (tppt) cc_final: 0.7386 (tmtt) outliers start: 1 outliers final: 0 residues processed: 44 average time/residue: 0.1816 time to fit residues: 9.4337 Evaluate side-chains 42 residues out of total 284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 42 time to evaluate : 0.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 31 random chunks: chunk 26 optimal weight: 1.9990 chunk 23 optimal weight: 0.5980 chunk 13 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 15 optimal weight: 0.0470 chunk 12 optimal weight: 0.5980 chunk 24 optimal weight: 0.9980 chunk 9 optimal weight: 0.6980 chunk 14 optimal weight: 0.7980 chunk 18 optimal weight: 0.7980 chunk 28 optimal weight: 0.7980 overall best weight: 0.5478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 6 GLN K 6 GLN K 38 HIS A 600 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8030 moved from start: 0.1303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 2688 Z= 0.239 Angle : 0.511 4.571 3630 Z= 0.281 Chirality : 0.041 0.156 388 Planarity : 0.004 0.033 456 Dihedral : 4.212 19.087 351 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 1.06 % Allowed : 8.45 % Favored : 90.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -0.73 (0.48), residues: 316 helix: 0.86 (0.50), residues: 77 sheet: -0.99 (0.54), residues: 104 loop : -0.70 (0.56), residues: 135 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP H 79 HIS 0.002 0.001 HIS A 660 PHE 0.011 0.002 PHE K 83 TYR 0.010 0.001 TYR K 49 ARG 0.004 0.001 ARG H 71 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 632 Ramachandran restraints generated. 316 Oldfield, 0 Emsley, 316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 632 Ramachandran restraints generated. 316 Oldfield, 0 Emsley, 316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 45 time to evaluate : 0.312 Fit side-chains REVERT: H 83 ARG cc_start: 0.7555 (mtt180) cc_final: 0.7048 (mtt-85) REVERT: A 680 LYS cc_start: 0.8130 (mtpt) cc_final: 0.7519 (mmmt) REVERT: A 706 LYS cc_start: 0.7811 (tppt) cc_final: 0.7244 (tmtt) outliers start: 3 outliers final: 1 residues processed: 46 average time/residue: 0.2269 time to fit residues: 12.0606 Evaluate side-chains 47 residues out of total 284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 46 time to evaluate : 0.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 102 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 31 random chunks: chunk 15 optimal weight: 0.9990 chunk 8 optimal weight: 2.9990 chunk 23 optimal weight: 0.9980 chunk 19 optimal weight: 0.5980 chunk 7 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 25 optimal weight: 0.6980 chunk 27 optimal weight: 0.1980 chunk 9 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 38 HIS A 600 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 0.1831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 2688 Z= 0.276 Angle : 0.521 4.622 3630 Z= 0.283 Chirality : 0.042 0.163 388 Planarity : 0.004 0.031 456 Dihedral : 4.229 17.315 351 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.33 % Favored : 93.67 % Rotamer: Outliers : 1.41 % Allowed : 11.27 % Favored : 87.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -0.23 (0.49), residues: 316 helix: 1.46 (0.53), residues: 82 sheet: -0.69 (0.55), residues: 101 loop : -0.62 (0.57), residues: 133 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP H 79 HIS 0.003 0.001 HIS A 660 PHE 0.010 0.002 PHE K 83 TYR 0.011 0.001 TYR K 49 ARG 0.002 0.000 ARG K 24 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 632 Ramachandran restraints generated. 316 Oldfield, 0 Emsley, 316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 632 Ramachandran restraints generated. 316 Oldfield, 0 Emsley, 316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 45 time to evaluate : 0.309 Fit side-chains revert: symmetry clash REVERT: H 83 ARG cc_start: 0.7568 (mtt180) cc_final: 0.7079 (mtt-85) REVERT: A 680 LYS cc_start: 0.8169 (mtpt) cc_final: 0.7601 (mmmt) REVERT: A 706 LYS cc_start: 0.7878 (tppt) cc_final: 0.7270 (tmtt) outliers start: 4 outliers final: 4 residues processed: 47 average time/residue: 0.2070 time to fit residues: 11.1889 Evaluate side-chains 49 residues out of total 284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 45 time to evaluate : 0.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 102 LEU Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 17 GLU Chi-restraints excluded: chain K residue 52 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 31 random chunks: chunk 27 optimal weight: 0.9990 chunk 21 optimal weight: 0.7980 chunk 14 optimal weight: 0.9990 chunk 3 optimal weight: 0.7980 chunk 13 optimal weight: 0.9980 chunk 18 optimal weight: 0.5980 chunk 28 optimal weight: 0.6980 chunk 29 optimal weight: 0.5980 chunk 26 optimal weight: 0.9980 chunk 8 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 moved from start: 0.2110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 2688 Z= 0.266 Angle : 0.491 4.571 3630 Z= 0.267 Chirality : 0.041 0.166 388 Planarity : 0.003 0.029 456 Dihedral : 4.191 15.920 351 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 2.82 % Allowed : 13.03 % Favored : 84.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: 0.02 (0.49), residues: 316 helix: 1.90 (0.54), residues: 82 sheet: -0.67 (0.54), residues: 101 loop : -0.52 (0.58), residues: 133 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP H 79 HIS 0.003 0.001 HIS A 660 PHE 0.010 0.002 PHE K 83 TYR 0.009 0.001 TYR K 49 ARG 0.002 0.000 ARG K 54 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 632 Ramachandran restraints generated. 316 Oldfield, 0 Emsley, 316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 632 Ramachandran restraints generated. 316 Oldfield, 0 Emsley, 316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 44 time to evaluate : 0.326 Fit side-chains revert: symmetry clash REVERT: H 31 ASP cc_start: 0.8285 (t0) cc_final: 0.7502 (t0) REVERT: H 83 ARG cc_start: 0.7609 (mtt180) cc_final: 0.7098 (mtt-85) REVERT: A 680 LYS cc_start: 0.8171 (mtpt) cc_final: 0.7619 (mmmt) REVERT: A 706 LYS cc_start: 0.7874 (tppt) cc_final: 0.7255 (tmtt) outliers start: 8 outliers final: 5 residues processed: 51 average time/residue: 0.1951 time to fit residues: 11.6940 Evaluate side-chains 50 residues out of total 284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 45 time to evaluate : 0.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 102 LEU Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 52 SER Chi-restraints excluded: chain K residue 74 THR Chi-restraints excluded: chain K residue 75 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 31 random chunks: chunk 17 optimal weight: 2.9990 chunk 0 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 12 optimal weight: 0.5980 chunk 25 optimal weight: 1.9990 chunk 20 optimal weight: 0.9980 chunk 15 optimal weight: 0.8980 chunk 26 optimal weight: 0.5980 chunk 7 optimal weight: 1.9990 chunk 10 optimal weight: 0.6980 chunk 5 optimal weight: 0.0980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 38 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 moved from start: 0.2259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 2688 Z= 0.227 Angle : 0.469 4.631 3630 Z= 0.253 Chirality : 0.040 0.163 388 Planarity : 0.003 0.029 456 Dihedral : 4.053 16.039 351 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 3.87 % Allowed : 11.97 % Favored : 84.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: 0.20 (0.50), residues: 316 helix: 2.34 (0.54), residues: 82 sheet: -0.66 (0.54), residues: 101 loop : -0.53 (0.57), residues: 133 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP K 96 HIS 0.003 0.001 HIS A 660 PHE 0.010 0.002 PHE K 83 TYR 0.009 0.001 TYR K 49 ARG 0.001 0.000 ARG K 54 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 632 Ramachandran restraints generated. 316 Oldfield, 0 Emsley, 316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 632 Ramachandran restraints generated. 316 Oldfield, 0 Emsley, 316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 43 time to evaluate : 0.323 Fit side-chains revert: symmetry clash REVERT: H 31 ASP cc_start: 0.8292 (t0) cc_final: 0.7525 (t0) REVERT: H 83 ARG cc_start: 0.7570 (mtt180) cc_final: 0.7098 (mtt-85) REVERT: K 6 GLN cc_start: 0.8428 (OUTLIER) cc_final: 0.7727 (mt0) REVERT: A 680 LYS cc_start: 0.8167 (mtpt) cc_final: 0.7625 (mmmt) REVERT: A 706 LYS cc_start: 0.7891 (tppt) cc_final: 0.7294 (tmtt) outliers start: 11 outliers final: 6 residues processed: 50 average time/residue: 0.1896 time to fit residues: 11.0865 Evaluate side-chains 50 residues out of total 284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 43 time to evaluate : 0.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 53 ILE Chi-restraints excluded: chain H residue 102 LEU Chi-restraints excluded: chain H residue 107 THR Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 6 GLN Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain K residue 33 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/phenix/phenix/programs/real_space_refine.py", line 213, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 766, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 67.5756 > 50: distance: 21 - 76: 23.350 distance: 24 - 73: 12.302 distance: 48 - 53: 15.030 distance: 53 - 54: 20.324 distance: 54 - 55: 14.677 distance: 54 - 57: 17.601 distance: 55 - 56: 8.933 distance: 55 - 61: 18.555 distance: 57 - 58: 28.395 distance: 58 - 59: 41.371 distance: 58 - 60: 28.803 distance: 61 - 62: 9.170 distance: 62 - 63: 10.591 distance: 62 - 65: 12.909 distance: 63 - 64: 26.596 distance: 63 - 67: 19.424 distance: 65 - 66: 17.745 distance: 67 - 68: 23.726 distance: 68 - 69: 27.003 distance: 68 - 71: 14.479 distance: 69 - 70: 35.599 distance: 69 - 73: 21.051 distance: 71 - 72: 16.098 distance: 72 - 199: 12.156 distance: 73 - 74: 11.934 distance: 74 - 75: 13.329 distance: 74 - 77: 17.547 distance: 75 - 76: 11.204 distance: 75 - 84: 15.943 distance: 77 - 78: 14.936 distance: 78 - 79: 25.160 distance: 79 - 80: 16.457 distance: 80 - 81: 5.803 distance: 81 - 82: 6.087 distance: 81 - 83: 5.656 distance: 84 - 85: 23.838 distance: 85 - 86: 28.813 distance: 85 - 88: 16.251 distance: 86 - 87: 10.835 distance: 86 - 89: 17.113 distance: 89 - 90: 14.005 distance: 90 - 91: 21.207 distance: 90 - 93: 23.567 distance: 91 - 92: 48.561 distance: 91 - 95: 9.289 distance: 93 - 94: 24.618 distance: 95 - 96: 37.918 distance: 96 - 97: 26.985 distance: 96 - 99: 35.708 distance: 97 - 104: 54.809 distance: 99 - 100: 31.187 distance: 100 - 101: 11.639 distance: 101 - 103: 33.146 distance: 104 - 105: 22.813 distance: 105 - 106: 36.715 distance: 105 - 108: 12.065 distance: 106 - 107: 41.841 distance: 106 - 110: 9.679 distance: 110 - 111: 33.576 distance: 111 - 112: 21.193 distance: 111 - 114: 48.300 distance: 112 - 113: 20.576 distance: 112 - 117: 17.874 distance: 114 - 115: 17.844 distance: 114 - 116: 42.475 distance: 117 - 118: 22.123 distance: 118 - 119: 25.821 distance: 119 - 120: 38.733 distance: 119 - 121: 15.028