Starting phenix.real_space_refine on Sat May 10 16:59:26 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wwk_32868/05_2025/7wwk_32868.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wwk_32868/05_2025/7wwk_32868.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7wwk_32868/05_2025/7wwk_32868.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wwk_32868/05_2025/7wwk_32868.map" model { file = "/net/cci-nas-00/data/ceres_data/7wwk_32868/05_2025/7wwk_32868.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wwk_32868/05_2025/7wwk_32868.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.003 sd= 0.028 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 30 5.16 5 C 4214 2.51 5 N 1116 2.21 5 O 1260 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 19 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 6620 Number of models: 1 Model: "" Number of chains: 6 Chain: "B" Number of atoms: 1550 Number of conformers: 1 Conformer: "" Number of residues, atoms: 193, 1550 Classifications: {'peptide': 193} Link IDs: {'PTRANS': 12, 'TRANS': 180} Chain: "C" Number of atoms: 1558 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1558 Classifications: {'peptide': 194} Link IDs: {'PTRANS': 12, 'TRANS': 181} Chain: "F" Number of atoms: 834 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 834 Classifications: {'peptide': 108} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 102} Chain: "G" Number of atoms: 922 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 922 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 3, 'TRANS': 117} Chain: "H" Number of atoms: 834 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 834 Classifications: {'peptide': 108} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 102} Chain: "I" Number of atoms: 922 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 922 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 3, 'TRANS': 117} Time building chain proxies: 6.62, per 1000 atoms: 1.00 Number of scatterers: 6620 At special positions: 0 Unit cell: (95.12, 107.42, 107.42, 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 30 16.00 O 1260 8.00 N 1116 7.00 C 4214 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=12, symmetry=0 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.02 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS F 23 " - pdb=" SG CYS F 88 " distance=2.03 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 23 " - pdb=" SG CYS H 88 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 96 " 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: 1.61 Conformation dependent library (CDL) restraints added in 967.0 milliseconds 1666 Ramachandran restraints generated. 833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1558 Finding SS restraints... Secondary structure from input PDB file: 15 helices and 18 sheets defined 10.2% alpha, 32.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.90 Creating SS restraints... Processing helix chain 'B' and resid 364 through 371 removed outlier: 3.615A pdb=" N VAL B 367 " --> pdb=" O ASP B 364 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N LEU B 371 " --> pdb=" O LEU B 368 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 387 removed outlier: 3.527A pdb=" N LEU B 387 " --> pdb=" O PRO B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 406 through 410 Processing helix chain 'B' and resid 417 through 422 Processing helix chain 'C' and resid 337 through 343 removed outlier: 3.909A pdb=" N VAL C 341 " --> pdb=" O PRO C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 366 through 371 Processing helix chain 'C' and resid 384 through 388 removed outlier: 3.571A pdb=" N LEU C 387 " --> pdb=" O PRO C 384 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 384 through 388' Processing helix chain 'C' and resid 404 through 410 removed outlier: 4.137A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ILE C 410 " --> pdb=" O VAL C 407 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 502 through 506 removed outlier: 3.560A pdb=" N GLN C 506 " --> pdb=" O VAL C 503 " (cutoff:3.500A) Processing helix chain 'F' and resid 79 through 83 removed outlier: 3.945A pdb=" N PHE F 83 " --> pdb=" O PRO F 80 " (cutoff:3.500A) Processing helix chain 'G' and resid 28 through 32 removed outlier: 3.764A pdb=" N SER G 31 " --> pdb=" O THR G 28 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N TYR G 32 " --> pdb=" O PHE G 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 28 through 32' Processing helix chain 'G' and resid 87 through 91 removed outlier: 4.144A pdb=" N THR G 91 " --> pdb=" O SER G 88 " (cutoff:3.500A) Processing helix chain 'H' and resid 79 through 83 removed outlier: 4.158A pdb=" N PHE H 83 " --> pdb=" O PRO H 80 " (cutoff:3.500A) Processing helix chain 'I' and resid 87 through 91 removed outlier: 4.142A pdb=" N THR I 91 " --> pdb=" O SER I 88 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 356 through 358 removed outlier: 4.287A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N GLU B 516 " --> pdb=" O ASN B 394 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 391 through 392 removed outlier: 3.542A pdb=" N PHE B 392 " --> pdb=" O VAL B 524 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AA4, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AA5, first strand: chain 'C' and resid 356 through 358 removed outlier: 3.583A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N GLU C 516 " --> pdb=" O ASN C 394 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 391 through 392 Processing sheet with id=AA7, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AA8, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AA9, first strand: chain 'F' and resid 4 through 7 Processing sheet with id=AB1, first strand: chain 'F' and resid 10 through 13 removed outlier: 6.547A pdb=" N LEU F 11 " --> pdb=" O GLU F 105 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N TRP F 35 " --> pdb=" O LEU F 47 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'G' and resid 3 through 6 Processing sheet with id=AB3, first strand: chain 'G' and resid 10 through 12 removed outlier: 6.651A pdb=" N PHE G 34 " --> pdb=" O ARG G 50 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N ARG G 50 " --> pdb=" O PHE G 34 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N TRP G 36 " --> pdb=" O MET G 48 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ILE G 57 " --> pdb=" O ILE G 52 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'G' and resid 10 through 12 removed outlier: 3.646A pdb=" N ASP G 110 " --> pdb=" O ARG G 98 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'H' and resid 4 through 7 Processing sheet with id=AB6, first strand: chain 'H' and resid 10 through 13 removed outlier: 3.561A pdb=" N ALA H 13 " --> pdb=" O GLU H 105 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N TRP H 35 " --> pdb=" O LEU H 47 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'I' and resid 3 through 6 Processing sheet with id=AB8, first strand: chain 'I' and resid 10 through 12 removed outlier: 8.673A pdb=" N TYR I 32 " --> pdb=" O ILE I 52 " (cutoff:3.500A) removed outlier: 5.866A pdb=" N ILE I 52 " --> pdb=" O TYR I 32 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N PHE I 34 " --> pdb=" O ARG I 50 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N ARG I 50 " --> pdb=" O PHE I 34 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N TRP I 36 " --> pdb=" O MET I 48 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'I' and resid 10 through 12 removed outlier: 3.623A pdb=" N ASP I 110 " --> pdb=" O ARG I 98 " (cutoff:3.500A) 222 hydrogen bonds defined for protein. 495 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.89 Time building geometry restraints manager: 1.88 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: 1912 1.33 - 1.45: 1282 1.45 - 1.57: 3560 1.57 - 1.69: 0 1.69 - 1.81: 36 Bond restraints: 6790 Sorted by residual: bond pdb=" C PHE C 392 " pdb=" N THR C 393 " ideal model delta sigma weight residual 1.335 1.403 -0.068 1.34e-02 5.57e+03 2.57e+01 bond pdb=" C CYS C 391 " pdb=" N PHE C 392 " ideal model delta sigma weight residual 1.331 1.390 -0.060 1.36e-02 5.41e+03 1.92e+01 bond pdb=" N CYS B 525 " pdb=" CA CYS B 525 " ideal model delta sigma weight residual 1.454 1.493 -0.040 1.23e-02 6.61e+03 1.04e+01 bond pdb=" N VAL B 341 " pdb=" CA VAL B 341 " ideal model delta sigma weight residual 1.456 1.490 -0.034 1.08e-02 8.57e+03 1.00e+01 bond pdb=" N LEU B 390 " pdb=" CA LEU B 390 " ideal model delta sigma weight residual 1.452 1.488 -0.036 1.25e-02 6.40e+03 8.29e+00 ... (remaining 6785 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.56: 8766 1.56 - 3.11: 378 3.11 - 4.67: 69 4.67 - 6.22: 3 6.22 - 7.78: 3 Bond angle restraints: 9219 Sorted by residual: angle pdb=" N VAL B 341 " pdb=" CA VAL B 341 " pdb=" C VAL B 341 " ideal model delta sigma weight residual 113.42 108.77 4.65 1.17e+00 7.31e-01 1.58e+01 angle pdb=" CA GLY G 99 " pdb=" C GLY G 99 " pdb=" O GLY G 99 " ideal model delta sigma weight residual 122.03 117.63 4.40 1.15e+00 7.56e-01 1.47e+01 angle pdb=" CA VAL I 107 " pdb=" C VAL I 107 " pdb=" O VAL I 107 " ideal model delta sigma weight residual 122.13 117.97 4.16 1.11e+00 8.12e-01 1.41e+01 angle pdb=" CA VAL B 524 " pdb=" C VAL B 524 " pdb=" O VAL B 524 " ideal model delta sigma weight residual 121.70 117.79 3.91 1.06e+00 8.90e-01 1.36e+01 angle pdb=" N ASN B 388 " pdb=" CA ASN B 388 " pdb=" C ASN B 388 " ideal model delta sigma weight residual 112.72 108.55 4.17 1.14e+00 7.69e-01 1.34e+01 ... (remaining 9214 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.00: 3659 18.00 - 35.99: 305 35.99 - 53.99: 42 53.99 - 71.99: 6 71.99 - 89.98: 5 Dihedral angle restraints: 4017 sinusoidal: 1564 harmonic: 2453 Sorted by residual: dihedral pdb=" CB CYS H 23 " pdb=" SG CYS H 23 " pdb=" SG CYS H 88 " pdb=" CB CYS H 88 " ideal model delta sinusoidal sigma weight residual 93.00 154.02 -61.02 1 1.00e+01 1.00e-02 4.95e+01 dihedral pdb=" CB CYS F 23 " pdb=" SG CYS F 23 " pdb=" SG CYS F 88 " pdb=" CB CYS F 88 " ideal model delta sinusoidal sigma weight residual 93.00 145.75 -52.75 1 1.00e+01 1.00e-02 3.79e+01 dihedral pdb=" CB CYS B 391 " pdb=" SG CYS B 391 " pdb=" SG CYS B 525 " pdb=" CB CYS B 525 " ideal model delta sinusoidal sigma weight residual 93.00 130.83 -37.83 1 1.00e+01 1.00e-02 2.02e+01 ... (remaining 4014 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 667 0.039 - 0.079: 199 0.079 - 0.118: 90 0.118 - 0.157: 27 0.157 - 0.196: 8 Chirality restraints: 991 Sorted by residual: chirality pdb=" CA ARG G 38 " pdb=" N ARG G 38 " pdb=" C ARG G 38 " pdb=" CB ARG G 38 " both_signs ideal model delta sigma weight residual False 2.51 2.71 -0.20 2.00e-01 2.50e+01 9.65e-01 chirality pdb=" CA VAL B 524 " pdb=" N VAL B 524 " pdb=" C VAL B 524 " pdb=" CB VAL B 524 " both_signs ideal model delta sigma weight residual False 2.44 2.63 -0.19 2.00e-01 2.50e+01 9.07e-01 chirality pdb=" CA VAL B 341 " pdb=" N VAL B 341 " pdb=" C VAL B 341 " pdb=" CB VAL B 341 " both_signs ideal model delta sigma weight residual False 2.44 2.62 -0.18 2.00e-01 2.50e+01 7.74e-01 ... (remaining 988 not shown) Planarity restraints: 1184 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY C 526 " 0.010 2.00e-02 2.50e+03 1.95e-02 3.80e+00 pdb=" C GLY C 526 " -0.034 2.00e-02 2.50e+03 pdb=" O GLY C 526 " 0.012 2.00e-02 2.50e+03 pdb=" N PRO C 527 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR B 523 " -0.009 2.00e-02 2.50e+03 1.88e-02 3.55e+00 pdb=" C THR B 523 " 0.033 2.00e-02 2.50e+03 pdb=" O THR B 523 " -0.012 2.00e-02 2.50e+03 pdb=" N VAL B 524 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP H 81 " 0.009 2.00e-02 2.50e+03 1.80e-02 3.24e+00 pdb=" CG ASP H 81 " -0.031 2.00e-02 2.50e+03 pdb=" OD1 ASP H 81 " 0.011 2.00e-02 2.50e+03 pdb=" OD2 ASP H 81 " 0.011 2.00e-02 2.50e+03 ... (remaining 1181 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.74: 518 2.74 - 3.28: 6207 3.28 - 3.82: 10069 3.82 - 4.36: 12376 4.36 - 4.90: 22292 Nonbonded interactions: 51462 Sorted by model distance: nonbonded pdb=" OG SER F 7 " pdb=" OG1 THR F 22 " model vdw 2.206 3.040 nonbonded pdb=" O GLY G 26 " pdb=" OH TYR G 32 " model vdw 2.243 3.040 nonbonded pdb=" OH TYR F 36 " pdb=" OE1 GLN F 89 " model vdw 2.267 3.040 nonbonded pdb=" NH1 ARG C 346 " pdb=" O PHE C 347 " model vdw 2.283 3.120 nonbonded pdb=" OH TYR H 36 " pdb=" OE1 GLN H 89 " model vdw 2.355 3.040 ... (remaining 51457 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 Found NCS groups: ncs_group { reference = chain 'B' selection = (chain 'C' and resid 335 through 527) } ncs_group { reference = chain 'F' selection = chain 'H' } ncs_group { reference = chain 'G' selection = chain 'I' } 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: 9.020 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: 0.000 Extract box with map and model: 0.280 Check model and map are aligned: 0.040 Set scattering table: 0.070 Process input model: 21.610 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8447 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 : 0.005 0.068 6802 Z= 0.293 Angle : 0.712 7.777 9243 Z= 0.449 Chirality : 0.050 0.196 991 Planarity : 0.004 0.032 1184 Dihedral : 12.679 89.981 2423 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.08 % Favored : 95.68 % Rotamer: Outliers : 0.00 % Allowed : 1.24 % Favored : 98.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -0.93 (0.29), residues: 833 helix: -3.93 (0.45), residues: 57 sheet: 0.12 (0.29), residues: 334 loop : -0.67 (0.30), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP G 36 HIS 0.004 0.001 HIS C 505 PHE 0.011 0.001 PHE C 347 TYR 0.011 0.001 TYR H 94 ARG 0.007 0.000 ARG I 87 Details of bonding type rmsd hydrogen bonds : bond 0.14457 ( 208) hydrogen bonds : angle 6.92539 ( 495) SS BOND : bond 0.00343 ( 12) SS BOND : angle 0.99174 ( 24) covalent geometry : bond 0.00452 ( 6790) covalent geometry : angle 0.71102 ( 9219) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1666 Ramachandran restraints generated. 833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1666 Ramachandran restraints generated. 833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 160 time to evaluate : 0.747 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 418 ILE cc_start: 0.9361 (mm) cc_final: 0.9156 (mt) REVERT: G 54 ILE cc_start: 0.9025 (tp) cc_final: 0.8812 (tp) outliers start: 0 outliers final: 0 residues processed: 160 average time/residue: 0.2182 time to fit residues: 44.4208 Evaluate side-chains 142 residues out of total 723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 142 time to evaluate : 0.748 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 69 optimal weight: 0.8980 chunk 62 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 21 optimal weight: 0.8980 chunk 41 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 64 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 39 optimal weight: 3.9990 chunk 47 optimal weight: 0.7980 chunk 74 optimal weight: 0.3980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 100 GLN ** G 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 109 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.084025 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2931 r_free = 0.2931 target = 0.070898 restraints weight = 14085.965| |-----------------------------------------------------------------------------| r_work (start): 0.2931 rms_B_bonded: 2.68 r_work: 0.2829 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2697 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.2697 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8834 moved from start: 0.1285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 6802 Z= 0.174 Angle : 0.561 7.218 9243 Z= 0.296 Chirality : 0.046 0.140 991 Planarity : 0.004 0.032 1184 Dihedral : 4.264 15.472 935 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 2.21 % Allowed : 9.27 % Favored : 88.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -0.86 (0.29), residues: 833 helix: -3.83 (0.45), residues: 57 sheet: 0.09 (0.29), residues: 338 loop : -0.56 (0.30), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP G 47 HIS 0.007 0.001 HIS C 505 PHE 0.012 0.001 PHE C 347 TYR 0.019 0.001 TYR H 94 ARG 0.005 0.000 ARG I 87 Details of bonding type rmsd hydrogen bonds : bond 0.03135 ( 208) hydrogen bonds : angle 5.76024 ( 495) SS BOND : bond 0.00207 ( 12) SS BOND : angle 0.88397 ( 24) covalent geometry : bond 0.00405 ( 6790) covalent geometry : angle 0.56027 ( 9219) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1666 Ramachandran restraints generated. 833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1666 Ramachandran restraints generated. 833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 145 time to evaluate : 0.744 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 54 ILE cc_start: 0.9170 (tp) cc_final: 0.8782 (mm) REVERT: I 3 GLN cc_start: 0.7741 (pm20) cc_final: 0.7297 (pm20) REVERT: I 35 ILE cc_start: 0.9347 (OUTLIER) cc_final: 0.9105 (mt) outliers start: 16 outliers final: 12 residues processed: 150 average time/residue: 0.2018 time to fit residues: 39.0230 Evaluate side-chains 152 residues out of total 723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 139 time to evaluate : 0.681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain F residue 5 THR Chi-restraints excluded: chain F residue 63 SER Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain F residue 78 LEU Chi-restraints excluded: chain G residue 38 ARG Chi-restraints excluded: chain G residue 91 THR Chi-restraints excluded: chain G residue 110 ASP Chi-restraints excluded: chain G residue 115 THR Chi-restraints excluded: chain H residue 19 VAL Chi-restraints excluded: chain I residue 35 ILE Chi-restraints excluded: chain I residue 57 ILE Chi-restraints excluded: chain I residue 100 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 36 optimal weight: 1.9990 chunk 62 optimal weight: 0.6980 chunk 60 optimal weight: 0.7980 chunk 57 optimal weight: 2.9990 chunk 80 optimal weight: 2.9990 chunk 68 optimal weight: 0.8980 chunk 51 optimal weight: 0.8980 chunk 10 optimal weight: 0.7980 chunk 42 optimal weight: 0.7980 chunk 47 optimal weight: 0.4980 chunk 45 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 43 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.084486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.071334 restraints weight = 14106.957| |-----------------------------------------------------------------------------| r_work (start): 0.2941 rms_B_bonded: 2.69 r_work: 0.2840 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2708 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.2708 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8827 moved from start: 0.1428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6802 Z= 0.132 Angle : 0.525 7.352 9243 Z= 0.276 Chirality : 0.044 0.142 991 Planarity : 0.004 0.038 1184 Dihedral : 4.121 14.189 935 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 2.21 % Allowed : 12.31 % Favored : 85.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -0.85 (0.29), residues: 833 helix: -4.09 (0.42), residues: 57 sheet: 0.14 (0.28), residues: 336 loop : -0.55 (0.30), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP G 47 HIS 0.005 0.001 HIS C 505 PHE 0.015 0.001 PHE G 29 TYR 0.013 0.001 TYR H 94 ARG 0.008 0.000 ARG I 98 Details of bonding type rmsd hydrogen bonds : bond 0.02865 ( 208) hydrogen bonds : angle 5.57309 ( 495) SS BOND : bond 0.00329 ( 12) SS BOND : angle 0.96667 ( 24) covalent geometry : bond 0.00307 ( 6790) covalent geometry : angle 0.52373 ( 9219) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1666 Ramachandran restraints generated. 833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1666 Ramachandran restraints generated. 833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 145 time to evaluate : 0.813 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 54 ILE cc_start: 0.9173 (tp) cc_final: 0.8785 (mm) REVERT: H 108 ARG cc_start: 0.4936 (ptt-90) cc_final: 0.4568 (ptt90) REVERT: I 3 GLN cc_start: 0.7713 (pm20) cc_final: 0.7233 (pm20) REVERT: I 35 ILE cc_start: 0.9336 (OUTLIER) cc_final: 0.9070 (mt) outliers start: 16 outliers final: 14 residues processed: 151 average time/residue: 0.2038 time to fit residues: 39.8724 Evaluate side-chains 150 residues out of total 723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 135 time to evaluate : 0.765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain F residue 5 THR Chi-restraints excluded: chain F residue 63 SER Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain F residue 78 LEU Chi-restraints excluded: chain F residue 81 ASP Chi-restraints excluded: chain G residue 38 ARG Chi-restraints excluded: chain G residue 43 GLN Chi-restraints excluded: chain G residue 57 ILE Chi-restraints excluded: chain G residue 91 THR Chi-restraints excluded: chain G residue 115 THR Chi-restraints excluded: chain H residue 19 VAL Chi-restraints excluded: chain I residue 35 ILE Chi-restraints excluded: chain I residue 57 ILE Chi-restraints excluded: chain I residue 100 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 75 optimal weight: 0.8980 chunk 71 optimal weight: 5.9990 chunk 46 optimal weight: 2.9990 chunk 53 optimal weight: 0.9990 chunk 56 optimal weight: 3.9990 chunk 6 optimal weight: 0.0980 chunk 78 optimal weight: 0.5980 chunk 49 optimal weight: 5.9990 chunk 31 optimal weight: 2.9990 chunk 1 optimal weight: 0.4980 chunk 26 optimal weight: 0.9980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 3 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.084858 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.071678 restraints weight = 14221.172| |-----------------------------------------------------------------------------| r_work (start): 0.2946 rms_B_bonded: 2.70 r_work: 0.2846 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2714 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.2714 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8823 moved from start: 0.1567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 6802 Z= 0.120 Angle : 0.512 7.070 9243 Z= 0.268 Chirality : 0.044 0.145 991 Planarity : 0.003 0.030 1184 Dihedral : 4.016 13.844 935 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 2.90 % Allowed : 13.97 % Favored : 83.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -0.79 (0.29), residues: 833 helix: -4.28 (0.41), residues: 51 sheet: 0.18 (0.29), residues: 334 loop : -0.54 (0.30), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP G 47 HIS 0.003 0.001 HIS C 505 PHE 0.022 0.001 PHE G 29 TYR 0.011 0.001 TYR H 91 ARG 0.006 0.000 ARG I 98 Details of bonding type rmsd hydrogen bonds : bond 0.02685 ( 208) hydrogen bonds : angle 5.42237 ( 495) SS BOND : bond 0.00198 ( 12) SS BOND : angle 1.08266 ( 24) covalent geometry : bond 0.00278 ( 6790) covalent geometry : angle 0.50922 ( 9219) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1666 Ramachandran restraints generated. 833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1666 Ramachandran restraints generated. 833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 141 time to evaluate : 0.790 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 406 GLU cc_start: 0.8530 (mt-10) cc_final: 0.8128 (mt-10) REVERT: F 100 GLN cc_start: 0.7896 (mp10) cc_final: 0.7654 (mt0) REVERT: H 108 ARG cc_start: 0.5015 (ptt-90) cc_final: 0.4666 (ptt90) REVERT: I 3 GLN cc_start: 0.7742 (pm20) cc_final: 0.7266 (pm20) REVERT: I 35 ILE cc_start: 0.9327 (OUTLIER) cc_final: 0.9064 (mt) outliers start: 21 outliers final: 15 residues processed: 151 average time/residue: 0.2089 time to fit residues: 40.9493 Evaluate side-chains 153 residues out of total 723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 137 time to evaluate : 0.700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain F residue 5 THR Chi-restraints excluded: chain F residue 20 THR Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain F residue 78 LEU Chi-restraints excluded: chain F residue 81 ASP Chi-restraints excluded: chain G residue 38 ARG Chi-restraints excluded: chain G residue 57 ILE Chi-restraints excluded: chain G residue 91 THR Chi-restraints excluded: chain G residue 110 ASP Chi-restraints excluded: chain G residue 115 THR Chi-restraints excluded: chain H residue 19 VAL Chi-restraints excluded: chain I residue 35 ILE Chi-restraints excluded: chain I residue 57 ILE Chi-restraints excluded: chain I residue 100 THR Chi-restraints excluded: chain I residue 118 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 59 optimal weight: 2.9990 chunk 65 optimal weight: 2.9990 chunk 4 optimal weight: 0.5980 chunk 58 optimal weight: 1.9990 chunk 34 optimal weight: 0.6980 chunk 67 optimal weight: 2.9990 chunk 23 optimal weight: 0.9990 chunk 38 optimal weight: 0.9990 chunk 13 optimal weight: 3.9990 chunk 33 optimal weight: 2.9990 chunk 75 optimal weight: 0.5980 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 43 GLN ** 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 = 0.3184 r_free = 0.3184 target = 0.084279 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.071082 restraints weight = 14248.788| |-----------------------------------------------------------------------------| r_work (start): 0.2934 rms_B_bonded: 2.70 r_work: 0.2834 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2704 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.2704 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8834 moved from start: 0.1695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6802 Z= 0.141 Angle : 0.529 6.861 9243 Z= 0.278 Chirality : 0.044 0.146 991 Planarity : 0.004 0.036 1184 Dihedral : 4.097 14.441 935 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 3.32 % Allowed : 14.52 % Favored : 82.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -0.84 (0.29), residues: 833 helix: -4.34 (0.40), residues: 51 sheet: 0.15 (0.29), residues: 336 loop : -0.58 (0.30), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP G 47 HIS 0.003 0.001 HIS C 505 PHE 0.031 0.001 PHE G 29 TYR 0.013 0.001 TYR H 91 ARG 0.009 0.000 ARG I 98 Details of bonding type rmsd hydrogen bonds : bond 0.02775 ( 208) hydrogen bonds : angle 5.38603 ( 495) SS BOND : bond 0.00227 ( 12) SS BOND : angle 1.10308 ( 24) covalent geometry : bond 0.00331 ( 6790) covalent geometry : angle 0.52704 ( 9219) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1666 Ramachandran restraints generated. 833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1666 Ramachandran restraints generated. 833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 142 time to evaluate : 0.904 Fit side-chains revert: symmetry clash REVERT: F 100 GLN cc_start: 0.7904 (mp10) cc_final: 0.7687 (mt0) REVERT: I 3 GLN cc_start: 0.7732 (pm20) cc_final: 0.7244 (pm20) REVERT: I 35 ILE cc_start: 0.9318 (OUTLIER) cc_final: 0.9041 (mt) REVERT: I 43 GLN cc_start: 0.9050 (mp10) cc_final: 0.8814 (mp10) outliers start: 24 outliers final: 18 residues processed: 154 average time/residue: 0.2123 time to fit residues: 42.5494 Evaluate side-chains 153 residues out of total 723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 134 time to evaluate : 0.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain F residue 5 THR Chi-restraints excluded: chain F residue 20 THR Chi-restraints excluded: chain F residue 63 SER Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain F residue 78 LEU Chi-restraints excluded: chain F residue 81 ASP Chi-restraints excluded: chain G residue 38 ARG Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain G residue 57 ILE Chi-restraints excluded: chain G residue 91 THR Chi-restraints excluded: chain G residue 110 ASP Chi-restraints excluded: chain G residue 115 THR Chi-restraints excluded: chain H residue 19 VAL Chi-restraints excluded: chain I residue 35 ILE Chi-restraints excluded: chain I residue 57 ILE Chi-restraints excluded: chain I residue 76 THR Chi-restraints excluded: chain I residue 100 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 79 optimal weight: 2.9990 chunk 6 optimal weight: 0.7980 chunk 29 optimal weight: 1.9990 chunk 37 optimal weight: 0.0970 chunk 26 optimal weight: 0.9980 chunk 74 optimal weight: 0.0970 chunk 62 optimal weight: 2.9990 chunk 48 optimal weight: 3.9990 chunk 75 optimal weight: 0.2980 chunk 46 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 overall best weight: 0.4576 ------------------------------------------------------------------------------- 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 = 0.3228 r_free = 0.3228 target = 0.086696 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.073708 restraints weight = 13987.734| |-----------------------------------------------------------------------------| r_work (start): 0.2984 rms_B_bonded: 2.65 r_work: 0.2884 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2751 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.2751 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8812 moved from start: 0.1785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 6802 Z= 0.101 Angle : 0.509 7.551 9243 Z= 0.264 Chirality : 0.043 0.144 991 Planarity : 0.003 0.035 1184 Dihedral : 3.885 13.277 935 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 2.77 % Allowed : 15.63 % Favored : 81.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -0.79 (0.30), residues: 833 helix: -4.22 (0.42), residues: 51 sheet: 0.15 (0.29), residues: 340 loop : -0.52 (0.30), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP G 47 HIS 0.003 0.000 HIS C 505 PHE 0.028 0.001 PHE G 29 TYR 0.012 0.001 TYR H 94 ARG 0.009 0.000 ARG I 98 Details of bonding type rmsd hydrogen bonds : bond 0.02553 ( 208) hydrogen bonds : angle 5.20809 ( 495) SS BOND : bond 0.00243 ( 12) SS BOND : angle 0.85493 ( 24) covalent geometry : bond 0.00234 ( 6790) covalent geometry : angle 0.50788 ( 9219) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1666 Ramachandran restraints generated. 833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1666 Ramachandran restraints generated. 833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 148 time to evaluate : 0.692 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 18 ARG cc_start: 0.8396 (ttm-80) cc_final: 0.8180 (ttt90) REVERT: G 69 THR cc_start: 0.8747 (t) cc_final: 0.8511 (t) REVERT: I 3 GLN cc_start: 0.7731 (pm20) cc_final: 0.7294 (pm20) REVERT: I 35 ILE cc_start: 0.9293 (OUTLIER) cc_final: 0.9027 (mt) outliers start: 20 outliers final: 16 residues processed: 158 average time/residue: 0.2127 time to fit residues: 43.2041 Evaluate side-chains 158 residues out of total 723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 141 time to evaluate : 0.663 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain F residue 20 THR Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain F residue 78 LEU Chi-restraints excluded: chain F residue 81 ASP Chi-restraints excluded: chain G residue 38 ARG Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain G residue 57 ILE Chi-restraints excluded: chain G residue 91 THR Chi-restraints excluded: chain G residue 115 THR Chi-restraints excluded: chain H residue 19 VAL Chi-restraints excluded: chain I residue 35 ILE Chi-restraints excluded: chain I residue 57 ILE Chi-restraints excluded: chain I residue 76 THR Chi-restraints excluded: chain I residue 100 THR Chi-restraints excluded: chain I residue 118 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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-5687/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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-5687/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-5687/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-5687/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-5687/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-5687/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-5687/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-5687/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-5687/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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-5687/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-5687/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-5687/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-5687/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: 64.6629 > 50: distance: 21 - 142: 16.680 distance: 22 - 136: 37.657 distance: 25 - 133: 21.515 distance: 65 - 75: 10.002 distance: 75 - 76: 22.160 distance: 76 - 77: 30.394 distance: 76 - 79: 28.326 distance: 77 - 78: 32.889 distance: 77 - 84: 15.966 distance: 79 - 80: 21.638 distance: 80 - 81: 18.087 distance: 81 - 82: 13.427 distance: 82 - 83: 9.032 distance: 84 - 85: 18.471 distance: 85 - 86: 37.006 distance: 85 - 88: 36.245 distance: 86 - 87: 4.705 distance: 86 - 92: 43.367 distance: 89 - 90: 23.208 distance: 89 - 91: 60.289 distance: 92 - 93: 36.296 distance: 92 - 98: 25.243 distance: 93 - 94: 10.900 distance: 94 - 95: 4.096 distance: 94 - 99: 18.935 distance: 96 - 97: 30.641 distance: 97 - 98: 40.271 distance: 99 - 100: 36.400 distance: 100 - 101: 18.299 distance: 100 - 103: 12.059 distance: 101 - 107: 7.379 distance: 103 - 104: 11.945 distance: 104 - 105: 4.399 distance: 104 - 106: 28.347 distance: 107 - 108: 13.628 distance: 108 - 109: 27.616 distance: 108 - 111: 12.515 distance: 109 - 110: 5.220 distance: 109 - 115: 20.332 distance: 111 - 112: 25.361 distance: 112 - 113: 21.095 distance: 112 - 114: 14.262 distance: 115 - 116: 27.167 distance: 116 - 117: 12.165 distance: 116 - 119: 18.350 distance: 117 - 118: 12.556 distance: 117 - 126: 19.131 distance: 119 - 120: 11.019 distance: 120 - 121: 16.312 distance: 120 - 122: 30.181 distance: 121 - 123: 18.217 distance: 122 - 124: 14.224 distance: 123 - 125: 11.052 distance: 124 - 125: 15.561 distance: 126 - 127: 26.037 distance: 127 - 128: 5.085 distance: 127 - 130: 6.616 distance: 128 - 129: 15.166 distance: 128 - 133: 8.493 distance: 130 - 131: 6.845 distance: 130 - 132: 6.855 distance: 133 - 134: 31.883 distance: 134 - 135: 31.290 distance: 135 - 136: 31.193 distance: 135 - 137: 21.818 distance: 137 - 138: 28.832 distance: 137 - 195: 20.278 distance: 138 - 139: 16.501 distance: 138 - 141: 26.899 distance: 139 - 140: 9.060 distance: 139 - 143: 10.008 distance: 140 - 192: 23.427 distance: 141 - 142: 11.722 distance: 143 - 144: 16.112 distance: 144 - 145: 8.665 distance: 144 - 147: 13.736 distance: 145 - 146: 14.550 distance: 145 - 150: 6.718 distance: 147 - 148: 14.166 distance: 147 - 149: 16.942