Starting phenix.real_space_refine on Thu Mar 6 02:08:30 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8k19_36789/03_2025/8k19_36789.cif Found real_map, /net/cci-nas-00/data/ceres_data/8k19_36789/03_2025/8k19_36789.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.88 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8k19_36789/03_2025/8k19_36789.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8k19_36789/03_2025/8k19_36789.map" model { file = "/net/cci-nas-00/data/ceres_data/8k19_36789/03_2025/8k19_36789.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8k19_36789/03_2025/8k19_36789.cif" } resolution = 3.88 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= 0.002 sd= 0.021 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 1446 atoms to isotropic. 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 19 5.16 5 C 2041 2.51 5 N 546 2.21 5 O 618 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 3224 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 906 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 906 Classifications: {'peptide': 119} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 114} Chain: "B" Number of atoms: 818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 818 Classifications: {'peptide': 107} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 100} Chain: "E" Number of atoms: 1500 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1500 Classifications: {'peptide': 188} Link IDs: {'PTRANS': 10, 'TRANS': 177} Chain breaks: 1 Time building chain proxies: 3.02, per 1000 atoms: 0.94 Number of scatterers: 3224 At special positions: 0 Unit cell: (61.48, 69.96, 94.34, 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 19 16.00 O 618 8.00 N 546 7.00 C 2041 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 22 " - pdb=" SG CYS A 95 " distance=2.03 Simple disulfide: pdb=" SG CYS B 23 " - pdb=" SG CYS B 88 " distance=2.03 Simple disulfide: pdb=" SG CYS E 336 " - pdb=" SG CYS E 361 " distance=2.03 Simple disulfide: pdb=" SG CYS E 379 " - pdb=" SG CYS E 432 " distance=2.05 Simple disulfide: pdb=" SG CYS E 391 " - pdb=" SG CYS E 525 " distance=2.04 Simple disulfide: pdb=" SG CYS E 480 " - pdb=" SG CYS E 488 " 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: 0.75 Conformation dependent library (CDL) restraints added in 395.7 milliseconds 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 756 Finding SS restraints... Secondary structure from input PDB file: 10 helices and 9 sheets defined 12.8% alpha, 38.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.50 Creating SS restraints... Processing helix chain 'A' and resid 28 through 32 Processing helix chain 'A' and resid 61 through 64 removed outlier: 3.507A pdb=" N LYS A 64 " --> pdb=" O ASP A 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 61 through 64' Processing helix chain 'A' and resid 86 through 90 Processing helix chain 'B' and resid 79 through 83 removed outlier: 3.877A pdb=" N ILE B 83 " --> pdb=" O PRO B 80 " (cutoff:3.500A) Processing helix chain 'E' and resid 338 through 343 Processing helix chain 'E' and resid 349 through 353 Processing helix chain 'E' and resid 365 through 370 Processing helix chain 'E' and resid 405 through 410 Processing helix chain 'E' and resid 416 through 422 Processing helix chain 'E' and resid 502 through 505 Processing sheet with id=AA1, first strand: chain 'A' and resid 4 through 7 removed outlier: 3.539A pdb=" N VAL A 5 " --> pdb=" O ALA A 23 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU A 80 " --> pdb=" O LEU A 20 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 57 through 59 removed outlier: 6.826A pdb=" N TRP A 36 " --> pdb=" O VAL A 48 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N ASP A 50 " --> pdb=" O MET A 34 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N MET A 34 " --> pdb=" O ASP A 50 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N VAL A 108 " --> pdb=" O ARG A 97 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 57 through 59 removed outlier: 6.826A pdb=" N TRP A 36 " --> pdb=" O VAL A 48 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N ASP A 50 " --> pdb=" O MET A 34 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N MET A 34 " --> pdb=" O ASP A 50 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 4 through 7 removed outlier: 3.939A pdb=" N HIS B 70 " --> pdb=" O SER B 67 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 10 through 13 removed outlier: 3.788A pdb=" N ALA B 84 " --> pdb=" O VAL B 104 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N TRP B 35 " --> pdb=" O LEU B 47 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 354 through 358 removed outlier: 3.658A pdb=" N GLU E 354 " --> pdb=" O SER E 399 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N VAL E 395 " --> pdb=" O ILE E 358 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLY E 431 " --> pdb=" O TYR E 380 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 354 through 358 removed outlier: 3.658A pdb=" N GLU E 354 " --> pdb=" O SER E 399 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N VAL E 395 " --> pdb=" O ILE E 358 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N PHE E 392 " --> pdb=" O VAL E 524 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N VAL E 524 " --> pdb=" O PHE E 392 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 452 through 454 Processing sheet with id=AA9, first strand: chain 'E' and resid 473 through 474 122 hydrogen bonds defined for protein. 300 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: 0.87 Time building geometry restraints manager: 0.91 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 782 1.33 - 1.46: 737 1.46 - 1.58: 1757 1.58 - 1.70: 1 1.70 - 1.82: 26 Bond restraints: 3303 Sorted by residual: bond pdb=" CB ASP B 1 " pdb=" CG ASP B 1 " ideal model delta sigma weight residual 1.516 1.631 -0.115 2.50e-02 1.60e+03 2.13e+01 bond pdb=" N GLY E 476 " pdb=" CA GLY E 476 " ideal model delta sigma weight residual 1.446 1.476 -0.030 9.50e-03 1.11e+04 1.01e+01 bond pdb=" CD2 HIS A 104 " pdb=" NE2 HIS A 104 " ideal model delta sigma weight residual 1.374 1.407 -0.033 1.10e-02 8.26e+03 8.78e+00 bond pdb=" CZ ARG B 61 " pdb=" NH2 ARG B 61 " ideal model delta sigma weight residual 1.330 1.292 0.038 1.30e-02 5.92e+03 8.56e+00 bond pdb=" N VAL E 382 " pdb=" CA VAL E 382 " ideal model delta sigma weight residual 1.455 1.490 -0.034 1.18e-02 7.18e+03 8.51e+00 ... (remaining 3298 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.65: 2953 1.65 - 3.30: 1198 3.30 - 4.94: 279 4.94 - 6.59: 41 6.59 - 8.24: 13 Bond angle restraints: 4484 Sorted by residual: angle pdb=" CA ASP A 107 " pdb=" CB ASP A 107 " pdb=" CG ASP A 107 " ideal model delta sigma weight residual 112.60 119.22 -6.62 1.00e+00 1.00e+00 4.39e+01 angle pdb=" OD1 ASN E 334 " pdb=" CG ASN E 334 " pdb=" ND2 ASN E 334 " ideal model delta sigma weight residual 122.60 116.66 5.94 1.00e+00 1.00e+00 3.53e+01 angle pdb=" CB HIS B 93 " pdb=" CG HIS B 93 " pdb=" CD2 HIS B 93 " ideal model delta sigma weight residual 131.20 123.49 7.71 1.30e+00 5.92e-01 3.52e+01 angle pdb=" OE1 GLN A 39 " pdb=" CD GLN A 39 " pdb=" NE2 GLN A 39 " ideal model delta sigma weight residual 122.60 117.01 5.59 1.00e+00 1.00e+00 3.12e+01 angle pdb=" OE1 GLN A 13 " pdb=" CD GLN A 13 " pdb=" NE2 GLN A 13 " ideal model delta sigma weight residual 122.60 117.11 5.49 1.00e+00 1.00e+00 3.02e+01 ... (remaining 4479 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.54: 1886 25.54 - 51.07: 63 51.07 - 76.61: 6 76.61 - 102.15: 1 102.15 - 127.68: 1 Dihedral angle restraints: 1957 sinusoidal: 765 harmonic: 1192 Sorted by residual: dihedral pdb=" C GLU A 26 " pdb=" N GLU A 26 " pdb=" CA GLU A 26 " pdb=" CB GLU A 26 " ideal model delta harmonic sigma weight residual -122.60 -138.49 15.89 0 2.50e+00 1.60e-01 4.04e+01 dihedral pdb=" CA ARG A 97 " pdb=" C ARG A 97 " pdb=" N PRO A 98 " pdb=" CA PRO A 98 " ideal model delta harmonic sigma weight residual 180.00 152.15 27.85 0 5.00e+00 4.00e-02 3.10e+01 dihedral pdb=" CA ASN A 32 " pdb=" C ASN A 32 " pdb=" N TYR A 33 " pdb=" CA TYR A 33 " ideal model delta harmonic sigma weight residual 180.00 153.59 26.41 0 5.00e+00 4.00e-02 2.79e+01 ... (remaining 1954 not shown) Histogram of chiral volume deviations from ideal: 0.001 - 0.112: 370 0.112 - 0.223: 105 0.223 - 0.334: 6 0.334 - 0.444: 1 0.444 - 0.555: 1 Chirality restraints: 483 Sorted by residual: chirality pdb=" CA GLU A 26 " pdb=" N GLU A 26 " pdb=" C GLU A 26 " pdb=" CB GLU A 26 " both_signs ideal model delta sigma weight residual False 2.51 1.96 0.56 2.00e-01 2.50e+01 7.71e+00 chirality pdb=" CA ASN E 487 " pdb=" N ASN E 487 " pdb=" C ASN E 487 " pdb=" CB ASN E 487 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.90e+00 chirality pdb=" CB THR E 523 " pdb=" CA THR E 523 " pdb=" OG1 THR E 523 " pdb=" CG2 THR E 523 " both_signs ideal model delta sigma weight residual False 2.55 2.27 0.28 2.00e-01 2.50e+01 2.00e+00 ... (remaining 480 not shown) Planarity restraints: 581 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB HIS B 93 " 0.135 2.00e-02 2.50e+03 1.07e-01 1.70e+02 pdb=" CG HIS B 93 " -0.115 2.00e-02 2.50e+03 pdb=" ND1 HIS B 93 " -0.115 2.00e-02 2.50e+03 pdb=" CD2 HIS B 93 " -0.078 2.00e-02 2.50e+03 pdb=" CE1 HIS B 93 " 0.121 2.00e-02 2.50e+03 pdb=" NE2 HIS B 93 " 0.052 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU B 105 " -0.057 2.00e-02 2.50e+03 1.20e-01 1.43e+02 pdb=" CD GLU B 105 " 0.207 2.00e-02 2.50e+03 pdb=" OE1 GLU B 105 " -0.075 2.00e-02 2.50e+03 pdb=" OE2 GLU B 105 " -0.075 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 59 " -0.137 2.00e-02 2.50e+03 7.20e-02 1.04e+02 pdb=" CG TYR A 59 " 0.057 2.00e-02 2.50e+03 pdb=" CD1 TYR A 59 " 0.084 2.00e-02 2.50e+03 pdb=" CD2 TYR A 59 " 0.047 2.00e-02 2.50e+03 pdb=" CE1 TYR A 59 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 TYR A 59 " 0.034 2.00e-02 2.50e+03 pdb=" CZ TYR A 59 " 0.004 2.00e-02 2.50e+03 pdb=" OH TYR A 59 " -0.093 2.00e-02 2.50e+03 ... (remaining 578 not shown) Histogram of nonbonded interaction distances: 1.50 - 2.18: 1 2.18 - 2.86: 956 2.86 - 3.54: 4394 3.54 - 4.22: 7933 4.22 - 4.90: 12972 Nonbonded interactions: 26256 Sorted by model distance: nonbonded pdb=" CD2 LEU E 455 " pdb=" OE1 GLN E 493 " model vdw 1.496 3.460 nonbonded pdb=" CZ PHE E 456 " pdb=" NE2 GLN E 493 " model vdw 2.507 3.420 nonbonded pdb=" OG1 THR A 56 " pdb=" OD2 ASP E 420 " model vdw 2.538 3.040 nonbonded pdb=" OD1 ASP E 442 " pdb=" OH TYR E 451 " model vdw 2.580 3.040 nonbonded pdb=" N PHE B 49 " pdb=" O PHE B 49 " model vdw 2.586 2.496 ... (remaining 26251 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.050 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.030 Construct map_model_manager: 0.000 Extract box with map and model: 0.140 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 13.530 Find NCS groups from input model: 0.040 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:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5336 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 : 0.014 0.115 3303 Z= 0.874 Angle : 1.836 8.239 4484 Z= 1.215 Chirality : 0.095 0.555 483 Planarity : 0.027 0.136 581 Dihedral : 13.091 127.681 1183 Min Nonbonded Distance : 1.496 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.74 % Allowed : 4.68 % Favored : 94.58 % Rotamer: Outliers : 0.57 % Allowed : 3.12 % Favored : 96.32 % Cbeta Deviations : 0.53 % 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: -1.84 (0.37), residues: 406 helix: -4.57 (0.30), residues: 24 sheet: -1.18 (0.39), residues: 122 loop : -0.87 (0.36), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.080 0.026 TRP A 36 HIS 0.052 0.012 HIS B 93 PHE 0.078 0.013 PHE E 497 TYR 0.137 0.031 TYR A 59 ARG 0.037 0.005 ARG A 35 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 29 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 27 time to evaluate : 0.392 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 MET cc_start: -0.0555 (mtm) cc_final: -0.1670 (mtt) outliers start: 2 outliers final: 0 residues processed: 29 average time/residue: 0.3132 time to fit residues: 10.4915 Evaluate side-chains 13 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 13 time to evaluate : 0.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 32 optimal weight: 10.0000 chunk 29 optimal weight: 3.9990 chunk 16 optimal weight: 6.9990 chunk 10 optimal weight: 6.9990 chunk 19 optimal weight: 20.0000 chunk 15 optimal weight: 6.9990 chunk 30 optimal weight: 4.9990 chunk 11 optimal weight: 6.9990 chunk 18 optimal weight: 10.0000 chunk 22 optimal weight: 4.9990 chunk 35 optimal weight: 30.0000 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 394 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.032536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.020123 restraints weight = 51011.604| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.020306 restraints weight = 48011.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.020357 restraints weight = 43485.088| |-----------------------------------------------------------------------------| r_work (final): 0.3225 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8328 moved from start: 0.3306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 3303 Z= 0.258 Angle : 0.659 6.946 4484 Z= 0.353 Chirality : 0.045 0.140 483 Planarity : 0.005 0.036 581 Dihedral : 5.583 34.216 457 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 17.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 0.00 % Allowed : 6.52 % Favored : 93.48 % 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: -1.03 (0.39), residues: 406 helix: -2.67 (0.81), residues: 32 sheet: -0.81 (0.41), residues: 128 loop : -0.22 (0.38), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 109 HIS 0.003 0.001 HIS B 70 PHE 0.015 0.002 PHE B 49 TYR 0.014 0.002 TYR A 33 ARG 0.003 0.001 ARG E 454 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 16 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 16 time to evaluate : 0.365 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 MET cc_start: 0.9325 (mpp) cc_final: 0.9043 (pmm) REVERT: A 82 MET cc_start: -0.0063 (mtm) cc_final: -0.0780 (mtt) outliers start: 0 outliers final: 0 residues processed: 16 average time/residue: 0.3049 time to fit residues: 5.8748 Evaluate side-chains 11 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 11 time to evaluate : 0.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 35 optimal weight: 3.9990 chunk 18 optimal weight: 9.9990 chunk 11 optimal weight: 3.9990 chunk 16 optimal weight: 8.9990 chunk 28 optimal weight: 20.0000 chunk 33 optimal weight: 9.9990 chunk 31 optimal weight: 8.9990 chunk 5 optimal weight: 0.0170 chunk 37 optimal weight: 0.8980 chunk 6 optimal weight: 10.0000 chunk 36 optimal weight: 5.9990 overall best weight: 2.9824 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.024961 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.020310 restraints weight = 73348.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.020172 restraints weight = 87901.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.020169 restraints weight = 100824.592| |-----------------------------------------------------------------------------| r_work (final): 0.3252 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 moved from start: 0.3813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 3303 Z= 0.164 Angle : 0.564 5.679 4484 Z= 0.300 Chirality : 0.044 0.140 483 Planarity : 0.004 0.032 581 Dihedral : 4.811 19.357 457 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 14.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 0.28 % Allowed : 6.52 % Favored : 93.20 % 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: -0.57 (0.41), residues: 406 helix: -2.67 (0.84), residues: 32 sheet: -0.33 (0.43), residues: 127 loop : 0.05 (0.40), residues: 247 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 109 HIS 0.001 0.001 HIS A 104 PHE 0.011 0.001 PHE B 49 TYR 0.009 0.001 TYR E 365 ARG 0.004 0.000 ARG E 454 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 14 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 13 time to evaluate : 0.392 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 MET cc_start: 0.7960 (ptt) cc_final: 0.7454 (ppp) outliers start: 1 outliers final: 0 residues processed: 14 average time/residue: 0.2995 time to fit residues: 5.1914 Evaluate side-chains 11 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 11 time to evaluate : 0.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 19 optimal weight: 30.0000 chunk 34 optimal weight: 20.0000 chunk 0 optimal weight: 30.0000 chunk 22 optimal weight: 10.0000 chunk 9 optimal weight: 10.0000 chunk 26 optimal weight: 10.0000 chunk 36 optimal weight: 6.9990 chunk 18 optimal weight: 50.0000 chunk 15 optimal weight: 10.0000 chunk 8 optimal weight: 30.0000 chunk 16 optimal weight: 7.9990 overall best weight: 8.9996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 70 HIS ** B 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 394 ASN ** E 505 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.024206 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 83)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.019518 restraints weight = 72330.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.019518 restraints weight = 92171.725| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.019518 restraints weight = 92172.203| |-----------------------------------------------------------------------------| r_work (final): 0.3227 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.6037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 3303 Z= 0.328 Angle : 0.680 6.095 4484 Z= 0.368 Chirality : 0.045 0.158 483 Planarity : 0.005 0.042 581 Dihedral : 5.552 21.730 457 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 29.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 0.57 % Allowed : 10.20 % Favored : 89.24 % 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: -1.10 (0.42), residues: 406 helix: -3.56 (0.61), residues: 44 sheet: -0.60 (0.42), residues: 141 loop : -0.03 (0.43), residues: 221 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 109 HIS 0.006 0.002 HIS E 505 PHE 0.014 0.003 PHE B 49 TYR 0.020 0.002 TYR E 365 ARG 0.009 0.001 ARG E 439 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 12 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 10 time to evaluate : 0.351 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 12 average time/residue: 0.2359 time to fit residues: 3.7172 Evaluate side-chains 10 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 9 time to evaluate : 0.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 446 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 24 optimal weight: 4.9990 chunk 29 optimal weight: 30.0000 chunk 13 optimal weight: 30.0000 chunk 34 optimal weight: 8.9990 chunk 33 optimal weight: 9.9990 chunk 30 optimal weight: 5.9990 chunk 27 optimal weight: 9.9990 chunk 0 optimal weight: 30.0000 chunk 32 optimal weight: 10.0000 chunk 8 optimal weight: 0.9980 chunk 5 optimal weight: 9.9990 overall best weight: 6.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 93 HIS ** E 505 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.024158 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.019322 restraints weight = 71398.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.019322 restraints weight = 89442.758| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.019322 restraints weight = 89442.758| |-----------------------------------------------------------------------------| r_work (final): 0.3223 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.6355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 3303 Z= 0.235 Angle : 0.598 8.464 4484 Z= 0.316 Chirality : 0.044 0.141 483 Planarity : 0.004 0.038 581 Dihedral : 5.246 20.304 457 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 24.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 1.13 % Allowed : 10.48 % Favored : 88.39 % 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: -1.02 (0.42), residues: 406 helix: -3.47 (0.62), residues: 44 sheet: -0.54 (0.43), residues: 142 loop : 0.02 (0.44), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 109 HIS 0.003 0.001 HIS B 38 PHE 0.013 0.002 PHE B 49 TYR 0.017 0.002 TYR E 380 ARG 0.005 0.001 ARG E 454 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 13 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 9 time to evaluate : 0.400 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 78 MET cc_start: 0.8366 (ptt) cc_final: 0.8149 (ppp) REVERT: A 106 MET cc_start: 0.6837 (tmm) cc_final: 0.5962 (tmm) outliers start: 4 outliers final: 2 residues processed: 13 average time/residue: 0.2193 time to fit residues: 3.8320 Evaluate side-chains 11 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 9 time to evaluate : 0.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain E residue 446 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 18 optimal weight: 7.9990 chunk 19 optimal weight: 9.9990 chunk 11 optimal weight: 30.0000 chunk 20 optimal weight: 5.9990 chunk 14 optimal weight: 5.9990 chunk 38 optimal weight: 8.9990 chunk 4 optimal weight: 10.0000 chunk 17 optimal weight: 6.9990 chunk 16 optimal weight: 10.0000 chunk 25 optimal weight: 7.9990 chunk 32 optimal weight: 20.0000 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 493 GLN ** E 505 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.023657 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.017228 restraints weight = 74522.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.017171 restraints weight = 79802.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.017171 restraints weight = 83719.754| |-----------------------------------------------------------------------------| r_work (final): 0.3148 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 moved from start: 0.7101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 3303 Z= 0.274 Angle : 0.668 15.349 4484 Z= 0.348 Chirality : 0.046 0.261 483 Planarity : 0.005 0.040 581 Dihedral : 5.435 22.277 457 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 27.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.65 % Favored : 93.35 % Rotamer: Outliers : 1.70 % Allowed : 11.05 % Favored : 87.25 % 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: -1.09 (0.43), residues: 406 helix: -3.37 (0.65), residues: 44 sheet: -0.61 (0.43), residues: 142 loop : -0.05 (0.45), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP A 36 HIS 0.005 0.001 HIS B 38 PHE 0.023 0.002 PHE E 377 TYR 0.014 0.002 TYR E 365 ARG 0.005 0.001 ARG E 454 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 15 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 9 time to evaluate : 3.888 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 78 MET cc_start: 0.8345 (ptt) cc_final: 0.7462 (ppp) outliers start: 6 outliers final: 3 residues processed: 15 average time/residue: 0.3198 time to fit residues: 7.2984 Evaluate side-chains 12 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 9 time to evaluate : 0.718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain B residue 92 ASP Chi-restraints excluded: chain E residue 446 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 21 optimal weight: 0.0030 chunk 24 optimal weight: 6.9990 chunk 0 optimal weight: 30.0000 chunk 12 optimal weight: 50.0000 chunk 23 optimal weight: 3.9990 chunk 30 optimal weight: 9.9990 chunk 33 optimal weight: 10.0000 chunk 31 optimal weight: 6.9990 chunk 8 optimal weight: 40.0000 chunk 26 optimal weight: 7.9990 chunk 22 optimal weight: 8.9990 overall best weight: 5.1998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.023591 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.017236 restraints weight = 72826.093| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.017236 restraints weight = 76260.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.017236 restraints weight = 76262.848| |-----------------------------------------------------------------------------| r_work (final): 0.3144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.7260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 3303 Z= 0.218 Angle : 0.694 22.380 4484 Z= 0.364 Chirality : 0.050 0.433 483 Planarity : 0.004 0.038 581 Dihedral : 5.298 22.645 457 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 23.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % Rotamer: Outliers : 1.70 % Allowed : 11.33 % Favored : 86.97 % 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: -1.06 (0.43), residues: 406 helix: -3.40 (0.65), residues: 44 sheet: -0.61 (0.43), residues: 139 loop : -0.01 (0.46), residues: 223 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 36 HIS 0.005 0.001 HIS B 38 PHE 0.012 0.002 PHE B 49 TYR 0.012 0.002 TYR E 365 ARG 0.003 0.000 ARG E 454 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 15 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 9 time to evaluate : 0.436 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 3 residues processed: 15 average time/residue: 0.2780 time to fit residues: 5.2749 Evaluate side-chains 12 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 9 time to evaluate : 0.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 92 ASP Chi-restraints excluded: chain E residue 368 LEU Chi-restraints excluded: chain E residue 446 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 20 optimal weight: 50.0000 chunk 28 optimal weight: 0.0470 chunk 19 optimal weight: 7.9990 chunk 35 optimal weight: 0.1980 chunk 4 optimal weight: 6.9990 chunk 10 optimal weight: 40.0000 chunk 0 optimal weight: 20.0000 chunk 31 optimal weight: 0.9990 chunk 18 optimal weight: 0.9980 chunk 11 optimal weight: 0.8980 chunk 34 optimal weight: 9.9990 overall best weight: 0.6280 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.023553 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.017143 restraints weight = 74536.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 16)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.017069 restraints weight = 79069.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.017055 restraints weight = 82878.606| |-----------------------------------------------------------------------------| r_work (final): 0.3098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8528 moved from start: 0.6830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 3303 Z= 0.147 Angle : 0.721 19.671 4484 Z= 0.365 Chirality : 0.045 0.209 483 Planarity : 0.004 0.034 581 Dihedral : 5.030 35.052 457 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 15.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 1.70 % Allowed : 11.33 % Favored : 86.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.26 % 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: -0.95 (0.43), residues: 406 helix: -3.53 (0.60), residues: 44 sheet: -0.45 (0.43), residues: 139 loop : 0.04 (0.45), residues: 223 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 36 HIS 0.005 0.001 HIS B 38 PHE 0.010 0.001 PHE B 49 TYR 0.015 0.001 TYR E 380 ARG 0.002 0.000 ARG A 19 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 17 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 11 time to evaluate : 0.467 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 MET cc_start: 0.9151 (mpp) cc_final: 0.8823 (mpp) REVERT: A 78 MET cc_start: 0.8341 (ptt) cc_final: 0.7331 (ppp) REVERT: E 438 THR cc_start: 0.8577 (OUTLIER) cc_final: 0.8270 (p) outliers start: 6 outliers final: 3 residues processed: 17 average time/residue: 0.4569 time to fit residues: 9.3794 Evaluate side-chains 15 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 11 time to evaluate : 0.997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 368 LEU Chi-restraints excluded: chain E residue 432 CYS Chi-restraints excluded: chain E residue 438 THR Chi-restraints excluded: chain E residue 446 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/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-5624/modules/cctbx_project/iotbx/cli_parser.py", line 980, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/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-5624/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/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-5624/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/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-5624/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-5624/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-5624/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-5624/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-5624/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-5624/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/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-5624/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-5624/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-5624/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-5624/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: 64.8999 > 50: distance: 6 - 9: 31.417 distance: 9 - 10: 45.950 distance: 10 - 11: 35.393 distance: 10 - 13: 19.233 distance: 11 - 12: 26.419 distance: 11 - 15: 13.417 distance: 13 - 14: 38.086 distance: 15 - 16: 21.038 distance: 15 - 137: 12.966 distance: 16 - 17: 24.551 distance: 16 - 19: 22.207 distance: 17 - 18: 16.977 distance: 17 - 23: 33.588 distance: 18 - 146: 21.567 distance: 19 - 20: 18.848 distance: 20 - 21: 19.951 distance: 20 - 22: 37.240 distance: 23 - 24: 19.538 distance: 24 - 25: 8.776 distance: 24 - 27: 25.846 distance: 25 - 26: 26.689 distance: 25 - 29: 18.828 distance: 29 - 30: 36.645 distance: 29 - 149: 22.595 distance: 30 - 31: 9.797 distance: 30 - 33: 8.494 distance: 31 - 32: 21.810 distance: 31 - 34: 20.970 distance: 35 - 36: 4.395 distance: 35 - 38: 11.370 distance: 36 - 37: 5.855 distance: 36 - 40: 11.720 distance: 38 - 39: 12.307 distance: 40 - 41: 17.184 distance: 41 - 42: 24.842 distance: 41 - 44: 22.206 distance: 42 - 43: 21.366 distance: 42 - 47: 8.862 distance: 44 - 45: 39.299 distance: 44 - 46: 24.368 distance: 47 - 48: 9.502 distance: 48 - 49: 6.071 distance: 49 - 50: 6.150 distance: 49 - 51: 36.087 distance: 51 - 52: 21.839 distance: 52 - 53: 21.529 distance: 52 - 55: 35.221 distance: 53 - 54: 15.295 distance: 53 - 59: 22.800 distance: 55 - 56: 16.909 distance: 56 - 57: 49.743 distance: 56 - 58: 24.290 distance: 59 - 60: 8.115 distance: 60 - 61: 29.321 distance: 60 - 63: 14.510 distance: 61 - 62: 13.565 distance: 61 - 70: 30.325 distance: 63 - 64: 28.008 distance: 64 - 65: 10.015 distance: 65 - 66: 7.069 distance: 66 - 67: 14.468 distance: 67 - 68: 22.537 distance: 67 - 69: 14.700 distance: 70 - 71: 10.380 distance: 70 - 100: 16.754 distance: 71 - 72: 8.826 distance: 71 - 74: 23.248 distance: 72 - 73: 29.110 distance: 72 - 77: 16.117 distance: 73 - 97: 19.095 distance: 74 - 75: 26.931 distance: 74 - 76: 9.117