Starting phenix.real_space_refine on Sat Apr 26 16:55:45 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dm0_27522/04_2025/8dm0_27522.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dm0_27522/04_2025/8dm0_27522.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.21 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8dm0_27522/04_2025/8dm0_27522.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dm0_27522/04_2025/8dm0_27522.map" model { file = "/net/cci-nas-00/data/ceres_data/8dm0_27522/04_2025/8dm0_27522.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dm0_27522/04_2025/8dm0_27522.cif" } resolution = 3.21 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.014 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 13 5.16 5 C 1582 2.51 5 N 414 2.21 5 O 471 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib" Total number of atoms: 2480 Number of models: 1 Model: "" Number of chains: 3 Chain: "C" Number of atoms: 1543 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1543 Classifications: {'peptide': 195} Link IDs: {'PTRANS': 11, 'TRANS': 183} Chain: "H" Number of atoms: 923 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 923 Classifications: {'peptide': 119} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 115} Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 3.78, per 1000 atoms: 1.52 Number of scatterers: 2480 At special positions: 0 Unit cell: (68, 81, 70, 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 13 16.00 O 471 8.00 N 414 7.00 C 1582 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 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=2.02 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 95 " 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 Links applied NAG-ASN " NAG C1301 " - " ASN C 343 " Time building additional restraints: 0.55 Conformation dependent library (CDL) restraints added in 300.1 milliseconds 620 Ramachandran restraints generated. 310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 572 Finding SS restraints... Secondary structure from input PDB file: 7 helices and 5 sheets defined 13.4% alpha, 27.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.33 Creating SS restraints... Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 365 through 370 removed outlier: 3.552A pdb=" N TYR C 369 " --> pdb=" O TYR C 365 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ASN C 370 " --> pdb=" O SER C 366 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 365 through 370' Processing helix chain 'C' and resid 384 through 389 removed outlier: 4.078A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 removed outlier: 4.276A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 438 through 443 Processing helix chain 'H' and resid 86 through 90 removed outlier: 3.512A pdb=" N ASP H 89 " --> pdb=" O ARG H 86 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N THR H 90 " --> pdb=" O ALA H 87 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 86 through 90' Processing sheet with id=AA1, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.647A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.710A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AA4, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AA5, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.129A pdb=" N GLY H 10 " --> pdb=" O THR H 116 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N MET H 34 " --> pdb=" O ASN H 50 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N ASN H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) 73 hydrogen bonds defined for protein. 183 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: 0.63 Time building geometry restraints manager: 0.68 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 786 1.34 - 1.46: 647 1.46 - 1.58: 1097 1.58 - 1.69: 1 1.69 - 1.81: 16 Bond restraints: 2547 Sorted by residual: bond pdb=" CB PRO H 14 " pdb=" CG PRO H 14 " ideal model delta sigma weight residual 1.492 1.613 -0.121 5.00e-02 4.00e+02 5.83e+00 bond pdb=" C1 NAG C1301 " pdb=" O5 NAG C1301 " ideal model delta sigma weight residual 1.406 1.450 -0.044 2.00e-02 2.50e+03 4.78e+00 bond pdb=" N ASP H 107 " pdb=" CA ASP H 107 " ideal model delta sigma weight residual 1.457 1.483 -0.026 1.29e-02 6.01e+03 4.04e+00 bond pdb=" CB GLU C 465 " pdb=" CG GLU C 465 " ideal model delta sigma weight residual 1.520 1.569 -0.049 3.00e-02 1.11e+03 2.72e+00 bond pdb=" CG GLU C 465 " pdb=" CD GLU C 465 " ideal model delta sigma weight residual 1.516 1.555 -0.039 2.50e-02 1.60e+03 2.40e+00 ... (remaining 2542 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.25: 3318 2.25 - 4.50: 126 4.50 - 6.74: 16 6.74 - 8.99: 4 8.99 - 11.24: 2 Bond angle restraints: 3466 Sorted by residual: angle pdb=" C TYR C 505 " pdb=" N GLN C 506 " pdb=" CA GLN C 506 " ideal model delta sigma weight residual 120.68 131.92 -11.24 1.52e+00 4.33e-01 5.47e+01 angle pdb=" CA PRO H 14 " pdb=" N PRO H 14 " pdb=" CD PRO H 14 " ideal model delta sigma weight residual 112.00 103.09 8.91 1.40e+00 5.10e-01 4.05e+01 angle pdb=" N PRO H 14 " pdb=" CA PRO H 14 " pdb=" C PRO H 14 " ideal model delta sigma weight residual 110.55 118.61 -8.06 1.63e+00 3.76e-01 2.45e+01 angle pdb=" CB GLU C 465 " pdb=" CG GLU C 465 " pdb=" CD GLU C 465 " ideal model delta sigma weight residual 112.60 119.56 -6.96 1.70e+00 3.46e-01 1.68e+01 angle pdb=" CA LEU H 63 " pdb=" CB LEU H 63 " pdb=" CG LEU H 63 " ideal model delta sigma weight residual 116.30 126.99 -10.69 3.50e+00 8.16e-02 9.33e+00 ... (remaining 3461 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.80: 1304 13.80 - 27.59: 143 27.59 - 41.39: 42 41.39 - 55.18: 7 55.18 - 68.98: 1 Dihedral angle restraints: 1497 sinusoidal: 590 harmonic: 907 Sorted by residual: dihedral pdb=" CA ASN C 487 " pdb=" C ASN C 487 " pdb=" N CYS C 488 " pdb=" CA CYS C 488 " ideal model delta harmonic sigma weight residual -180.00 -154.32 -25.68 0 5.00e+00 4.00e-02 2.64e+01 dihedral pdb=" CB CYS C 480 " pdb=" SG CYS C 480 " pdb=" SG CYS C 488 " pdb=" CB CYS C 488 " ideal model delta sinusoidal sigma weight residual 93.00 132.19 -39.19 1 1.00e+01 1.00e-02 2.16e+01 dihedral pdb=" CA VAL C 483 " pdb=" C VAL C 483 " pdb=" N GLU C 484 " pdb=" CA GLU C 484 " ideal model delta harmonic sigma weight residual 180.00 -158.37 -21.63 0 5.00e+00 4.00e-02 1.87e+01 ... (remaining 1494 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 280 0.061 - 0.122: 77 0.122 - 0.183: 10 0.183 - 0.243: 2 0.243 - 0.304: 2 Chirality restraints: 371 Sorted by residual: chirality pdb=" CA PRO H 14 " pdb=" N PRO H 14 " pdb=" C PRO H 14 " pdb=" CB PRO H 14 " both_signs ideal model delta sigma weight residual False 2.72 2.41 0.30 2.00e-01 2.50e+01 2.31e+00 chirality pdb=" CB THR C 470 " pdb=" CA THR C 470 " pdb=" OG1 THR C 470 " pdb=" CG2 THR C 470 " both_signs ideal model delta sigma weight residual False 2.55 2.26 0.29 2.00e-01 2.50e+01 2.10e+00 chirality pdb=" CA ASN C 440 " pdb=" N ASN C 440 " pdb=" C ASN C 440 " pdb=" CB ASN C 440 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 8.75e-01 ... (remaining 368 not shown) Planarity restraints: 448 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN H 13 " -0.058 5.00e-02 4.00e+02 8.28e-02 1.10e+01 pdb=" N PRO H 14 " 0.143 5.00e-02 4.00e+02 pdb=" CA PRO H 14 " -0.039 5.00e-02 4.00e+02 pdb=" CD PRO H 14 " -0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 473 " -0.013 2.00e-02 2.50e+03 1.86e-02 6.95e+00 pdb=" CG TYR C 473 " 0.046 2.00e-02 2.50e+03 pdb=" CD1 TYR C 473 " -0.013 2.00e-02 2.50e+03 pdb=" CD2 TYR C 473 " -0.018 2.00e-02 2.50e+03 pdb=" CE1 TYR C 473 " -0.005 2.00e-02 2.50e+03 pdb=" CE2 TYR C 473 " -0.000 2.00e-02 2.50e+03 pdb=" CZ TYR C 473 " 0.000 2.00e-02 2.50e+03 pdb=" OH TYR C 473 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA C 520 " -0.038 5.00e-02 4.00e+02 5.78e-02 5.35e+00 pdb=" N PRO C 521 " 0.100 5.00e-02 4.00e+02 pdb=" CA PRO C 521 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO C 521 " -0.032 5.00e-02 4.00e+02 ... (remaining 445 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 703 2.81 - 3.33: 1952 3.33 - 3.86: 3972 3.86 - 4.38: 4564 4.38 - 4.90: 8063 Nonbonded interactions: 19254 Sorted by model distance: nonbonded pdb=" OD1 ASN C 450 " pdb=" OG SER H 56 " model vdw 2.288 3.040 nonbonded pdb=" NE ARG C 457 " pdb=" OD2 ASP C 467 " model vdw 2.401 3.120 nonbonded pdb=" O4 NAG C1301 " pdb=" O6 NAG C1301 " model vdw 2.486 3.040 nonbonded pdb=" O ILE C 418 " pdb=" N TYR C 423 " model vdw 2.514 3.120 nonbonded pdb=" NH2 ARG C 454 " pdb=" O ASP C 467 " model vdw 2.528 3.120 ... (remaining 19249 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.600 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.100 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 13.180 Find NCS groups from input model: 0.020 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:3.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.121 2553 Z= 0.271 Angle : 1.011 11.238 3479 Z= 0.567 Chirality : 0.060 0.304 371 Planarity : 0.009 0.083 447 Dihedral : 12.719 68.980 910 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 0.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 0.00 % Allowed : 0.75 % Favored : 99.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.78 (0.40), residues: 310 helix: -4.74 (0.24), residues: 26 sheet: -0.29 (0.50), residues: 96 loop : -1.12 (0.37), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP H 109 HIS 0.007 0.002 HIS H 35 PHE 0.020 0.003 PHE C 497 TYR 0.046 0.002 TYR C 473 ARG 0.012 0.001 ARG H 19 Details of bonding type rmsd link_NAG-ASN : bond 0.00526 ( 1) link_NAG-ASN : angle 2.40853 ( 3) hydrogen bonds : bond 0.13297 ( 73) hydrogen bonds : angle 9.34903 ( 183) SS BOND : bond 0.00310 ( 5) SS BOND : angle 1.72891 ( 10) covalent geometry : bond 0.00619 ( 2547) covalent geometry : angle 1.00581 ( 3466) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 620 Ramachandran restraints generated. 310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 620 Ramachandran restraints generated. 310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 81 time to evaluate : 0.285 Fit side-chains revert: symmetry clash REVERT: H 60 ASN cc_start: 0.9086 (t0) cc_final: 0.8884 (t0) REVERT: H 98 VAL cc_start: 0.8299 (m) cc_final: 0.8026 (t) outliers start: 0 outliers final: 0 residues processed: 81 average time/residue: 0.1790 time to fit residues: 16.5891 Evaluate side-chains 76 residues out of total 267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 76 time to evaluate : 0.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 25 optimal weight: 0.1980 chunk 22 optimal weight: 0.9990 chunk 12 optimal weight: 0.9980 chunk 7 optimal weight: 1.9990 chunk 15 optimal weight: 0.9980 chunk 23 optimal weight: 0.0980 chunk 9 optimal weight: 0.6980 chunk 14 optimal weight: 0.0770 chunk 17 optimal weight: 1.9990 chunk 27 optimal weight: 0.9990 chunk 8 optimal weight: 0.4980 overall best weight: 0.3138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 35 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 = 0.3573 r_free = 0.3573 target = 0.119130 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.102229 restraints weight = 4568.760| |-----------------------------------------------------------------------------| r_work (start): 0.3319 rms_B_bonded: 3.27 r_work: 0.3199 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3199 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 moved from start: 0.1703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 2553 Z= 0.109 Angle : 0.584 9.495 3479 Z= 0.294 Chirality : 0.045 0.143 371 Planarity : 0.005 0.043 447 Dihedral : 5.594 27.578 372 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 0.37 % Allowed : 10.11 % Favored : 89.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.35 (0.41), residues: 310 helix: -3.56 (0.64), residues: 26 sheet: -0.19 (0.50), residues: 96 loop : -0.85 (0.37), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 436 HIS 0.002 0.001 HIS H 35 PHE 0.010 0.001 PHE C 377 TYR 0.010 0.001 TYR H 79 ARG 0.004 0.000 ARG C 466 Details of bonding type rmsd link_NAG-ASN : bond 0.00441 ( 1) link_NAG-ASN : angle 1.59931 ( 3) hydrogen bonds : bond 0.03124 ( 73) hydrogen bonds : angle 7.23811 ( 183) SS BOND : bond 0.00194 ( 5) SS BOND : angle 0.51303 ( 10) covalent geometry : bond 0.00257 ( 2547) covalent geometry : angle 0.58293 ( 3466) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 620 Ramachandran restraints generated. 310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 620 Ramachandran restraints generated. 310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 83 time to evaluate : 0.264 Fit side-chains REVERT: C 417 LYS cc_start: 0.8334 (mmtp) cc_final: 0.7962 (mtpt) REVERT: H 13 GLN cc_start: 0.8339 (mp10) cc_final: 0.8123 (mp10) REVERT: H 19 ARG cc_start: 0.7971 (ttm-80) cc_final: 0.7548 (tpp80) REVERT: H 60 ASN cc_start: 0.9212 (t0) cc_final: 0.8766 (t0) outliers start: 1 outliers final: 1 residues processed: 83 average time/residue: 0.1863 time to fit residues: 17.6766 Evaluate side-chains 76 residues out of total 267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 75 time to evaluate : 0.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 486 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 0 optimal weight: 2.9990 chunk 4 optimal weight: 1.9990 chunk 18 optimal weight: 0.0770 chunk 23 optimal weight: 0.4980 chunk 19 optimal weight: 3.9990 chunk 22 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 2 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 14 optimal weight: 0.5980 chunk 17 optimal weight: 0.0030 overall best weight: 0.6350 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 35 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 = 0.3528 r_free = 0.3528 target = 0.115599 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.099498 restraints weight = 4478.914| |-----------------------------------------------------------------------------| r_work (start): 0.3292 rms_B_bonded: 3.06 r_work: 0.3171 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.2106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 2553 Z= 0.148 Angle : 0.600 7.205 3479 Z= 0.298 Chirality : 0.044 0.138 371 Planarity : 0.004 0.036 447 Dihedral : 5.067 21.208 372 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 3.00 % Allowed : 11.61 % Favored : 85.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.24 (0.42), residues: 310 helix: -3.30 (0.77), residues: 27 sheet: -0.08 (0.50), residues: 96 loop : -0.81 (0.39), residues: 187 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 436 HIS 0.002 0.001 HIS H 35 PHE 0.024 0.002 PHE C 456 TYR 0.013 0.001 TYR C 473 ARG 0.005 0.000 ARG C 466 Details of bonding type rmsd link_NAG-ASN : bond 0.00372 ( 1) link_NAG-ASN : angle 1.46496 ( 3) hydrogen bonds : bond 0.03102 ( 73) hydrogen bonds : angle 6.78798 ( 183) SS BOND : bond 0.00107 ( 5) SS BOND : angle 0.64571 ( 10) covalent geometry : bond 0.00340 ( 2547) covalent geometry : angle 0.59819 ( 3466) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 620 Ramachandran restraints generated. 310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 620 Ramachandran restraints generated. 310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 81 time to evaluate : 0.280 Fit side-chains REVERT: C 417 LYS cc_start: 0.8421 (mmtp) cc_final: 0.8022 (mtpt) REVERT: H 13 GLN cc_start: 0.8485 (mp10) cc_final: 0.8263 (mp10) REVERT: H 19 ARG cc_start: 0.8028 (ttm-80) cc_final: 0.7574 (tpp80) REVERT: H 60 ASN cc_start: 0.9149 (t0) cc_final: 0.8715 (t0) outliers start: 8 outliers final: 5 residues processed: 85 average time/residue: 0.2005 time to fit residues: 19.3422 Evaluate side-chains 80 residues out of total 267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 75 time to evaluate : 0.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 486 PHE Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 98 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 14 optimal weight: 0.8980 chunk 18 optimal weight: 1.9990 chunk 15 optimal weight: 0.7980 chunk 20 optimal weight: 3.9990 chunk 8 optimal weight: 1.9990 chunk 7 optimal weight: 0.7980 chunk 29 optimal weight: 0.6980 chunk 28 optimal weight: 2.9990 chunk 22 optimal weight: 0.8980 chunk 10 optimal weight: 0.7980 chunk 27 optimal weight: 2.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 35 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 = 0.3513 r_free = 0.3513 target = 0.114325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.098270 restraints weight = 4671.647| |-----------------------------------------------------------------------------| r_work (start): 0.3254 rms_B_bonded: 3.11 r_work: 0.3135 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3135 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 0.2358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 2553 Z= 0.176 Angle : 0.592 5.748 3479 Z= 0.298 Chirality : 0.045 0.136 371 Planarity : 0.004 0.034 447 Dihedral : 5.077 20.037 372 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 2.62 % Allowed : 13.48 % Favored : 83.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.33 (0.42), residues: 310 helix: -3.12 (0.88), residues: 27 sheet: -0.23 (0.50), residues: 91 loop : -0.85 (0.38), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 436 HIS 0.001 0.001 HIS H 53 PHE 0.011 0.001 PHE C 377 TYR 0.012 0.001 TYR C 473 ARG 0.003 0.001 ARG H 97 Details of bonding type rmsd link_NAG-ASN : bond 0.00283 ( 1) link_NAG-ASN : angle 1.41211 ( 3) hydrogen bonds : bond 0.03162 ( 73) hydrogen bonds : angle 6.70921 ( 183) SS BOND : bond 0.00185 ( 5) SS BOND : angle 0.58984 ( 10) covalent geometry : bond 0.00402 ( 2547) covalent geometry : angle 0.59103 ( 3466) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 620 Ramachandran restraints generated. 310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 620 Ramachandran restraints generated. 310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 76 time to evaluate : 0.299 Fit side-chains REVERT: C 417 LYS cc_start: 0.8424 (mmtp) cc_final: 0.8033 (mtpt) REVERT: H 19 ARG cc_start: 0.8065 (ttm-80) cc_final: 0.7555 (tpp80) REVERT: H 60 ASN cc_start: 0.9178 (t0) cc_final: 0.8751 (t0) REVERT: H 106 MET cc_start: 0.8397 (OUTLIER) cc_final: 0.8169 (mtt) outliers start: 7 outliers final: 5 residues processed: 78 average time/residue: 0.2057 time to fit residues: 18.1746 Evaluate side-chains 79 residues out of total 267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 73 time to evaluate : 0.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 486 PHE Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 98 VAL Chi-restraints excluded: chain H residue 106 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 23 optimal weight: 0.0070 chunk 3 optimal weight: 2.9990 chunk 0 optimal weight: 1.9990 chunk 1 optimal weight: 0.4980 chunk 28 optimal weight: 0.8980 chunk 16 optimal weight: 1.9990 chunk 4 optimal weight: 0.7980 chunk 2 optimal weight: 0.5980 chunk 25 optimal weight: 0.0370 chunk 17 optimal weight: 0.0980 chunk 29 optimal weight: 0.8980 overall best weight: 0.2476 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 35 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 = 0.3572 r_free = 0.3572 target = 0.118526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.101925 restraints weight = 4645.576| |-----------------------------------------------------------------------------| r_work (start): 0.3324 rms_B_bonded: 3.23 r_work: 0.3202 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3202 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.2542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 2553 Z= 0.096 Angle : 0.538 5.075 3479 Z= 0.268 Chirality : 0.043 0.132 371 Planarity : 0.004 0.034 447 Dihedral : 4.483 17.239 372 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 1.87 % Allowed : 16.48 % Favored : 81.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.23 (0.42), residues: 310 helix: -3.25 (0.81), residues: 27 sheet: -0.13 (0.50), residues: 91 loop : -0.75 (0.39), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 436 HIS 0.001 0.001 HIS H 53 PHE 0.008 0.001 PHE C 377 TYR 0.008 0.001 TYR C 473 ARG 0.005 0.000 ARG C 403 Details of bonding type rmsd link_NAG-ASN : bond 0.00369 ( 1) link_NAG-ASN : angle 1.24019 ( 3) hydrogen bonds : bond 0.02849 ( 73) hydrogen bonds : angle 6.40439 ( 183) SS BOND : bond 0.00180 ( 5) SS BOND : angle 0.55401 ( 10) covalent geometry : bond 0.00226 ( 2547) covalent geometry : angle 0.53649 ( 3466) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 620 Ramachandran restraints generated. 310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 620 Ramachandran restraints generated. 310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 75 time to evaluate : 0.324 Fit side-chains REVERT: C 417 LYS cc_start: 0.8413 (mmtp) cc_final: 0.8011 (mtpt) REVERT: H 19 ARG cc_start: 0.8064 (ttm-80) cc_final: 0.7630 (tpp80) REVERT: H 60 ASN cc_start: 0.9156 (t0) cc_final: 0.8782 (t0) REVERT: H 66 LEU cc_start: 0.7970 (mt) cc_final: 0.7759 (mm) REVERT: H 81 GLN cc_start: 0.8567 (tp40) cc_final: 0.7804 (tp40) outliers start: 5 outliers final: 4 residues processed: 77 average time/residue: 0.1965 time to fit residues: 17.2653 Evaluate side-chains 75 residues out of total 267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 71 time to evaluate : 0.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 486 PHE Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 98 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 18 optimal weight: 0.5980 chunk 23 optimal weight: 0.7980 chunk 5 optimal weight: 0.9990 chunk 17 optimal weight: 0.7980 chunk 4 optimal weight: 0.7980 chunk 27 optimal weight: 1.9990 chunk 29 optimal weight: 0.5980 chunk 0 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 2 optimal weight: 2.9990 chunk 21 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: ** H 35 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 = 0.3518 r_free = 0.3518 target = 0.114766 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.098398 restraints weight = 4686.122| |-----------------------------------------------------------------------------| r_work (start): 0.3259 rms_B_bonded: 3.14 r_work: 0.3139 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3139 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.2650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 2553 Z= 0.161 Angle : 0.596 6.766 3479 Z= 0.294 Chirality : 0.044 0.131 371 Planarity : 0.004 0.034 447 Dihedral : 4.621 16.922 372 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 3.37 % Allowed : 16.48 % Favored : 80.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.19 (0.43), residues: 310 helix: -3.01 (0.90), residues: 27 sheet: -0.09 (0.51), residues: 91 loop : -0.77 (0.39), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP H 47 HIS 0.001 0.001 HIS H 35 PHE 0.010 0.001 PHE C 377 TYR 0.011 0.001 TYR H 79 ARG 0.004 0.001 ARG C 403 Details of bonding type rmsd link_NAG-ASN : bond 0.00263 ( 1) link_NAG-ASN : angle 1.31075 ( 3) hydrogen bonds : bond 0.03038 ( 73) hydrogen bonds : angle 6.43171 ( 183) SS BOND : bond 0.00144 ( 5) SS BOND : angle 0.48756 ( 10) covalent geometry : bond 0.00372 ( 2547) covalent geometry : angle 0.59479 ( 3466) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 620 Ramachandran restraints generated. 310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 620 Ramachandran restraints generated. 310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 69 time to evaluate : 0.277 Fit side-chains REVERT: C 417 LYS cc_start: 0.8439 (mmtp) cc_final: 0.8046 (mtpt) REVERT: H 19 ARG cc_start: 0.8079 (ttm-80) cc_final: 0.7445 (tpp80) REVERT: H 60 ASN cc_start: 0.9185 (t0) cc_final: 0.8780 (t0) REVERT: H 66 LEU cc_start: 0.8023 (mt) cc_final: 0.7803 (mm) REVERT: H 81 GLN cc_start: 0.8552 (tp40) cc_final: 0.7701 (tp40) REVERT: H 106 MET cc_start: 0.8394 (OUTLIER) cc_final: 0.8167 (mtt) outliers start: 9 outliers final: 6 residues processed: 73 average time/residue: 0.2137 time to fit residues: 17.6635 Evaluate side-chains 76 residues out of total 267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 69 time to evaluate : 0.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 486 PHE Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 98 VAL Chi-restraints excluded: chain H residue 106 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 23 optimal weight: 0.0070 chunk 0 optimal weight: 2.9990 chunk 3 optimal weight: 0.0370 chunk 27 optimal weight: 0.3980 chunk 16 optimal weight: 2.9990 chunk 29 optimal weight: 0.7980 chunk 18 optimal weight: 0.0980 chunk 2 optimal weight: 1.9990 chunk 6 optimal weight: 0.9990 chunk 21 optimal weight: 0.7980 chunk 11 optimal weight: 1.9990 overall best weight: 0.2676 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 35 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 = 0.3577 r_free = 0.3577 target = 0.118520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.102273 restraints weight = 4709.248| |-----------------------------------------------------------------------------| r_work (start): 0.3323 rms_B_bonded: 3.16 r_work: 0.3202 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3202 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.2849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 2553 Z= 0.102 Angle : 0.553 6.113 3479 Z= 0.275 Chirality : 0.043 0.129 371 Planarity : 0.003 0.034 447 Dihedral : 4.201 16.438 372 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 1.87 % Allowed : 17.98 % Favored : 80.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.90 (0.44), residues: 310 helix: -3.00 (0.86), residues: 27 sheet: 0.21 (0.52), residues: 90 loop : -0.60 (0.40), residues: 193 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 436 HIS 0.001 0.000 HIS H 35 PHE 0.008 0.001 PHE C 377 TYR 0.008 0.001 TYR C 473 ARG 0.003 0.000 ARG C 403 Details of bonding type rmsd link_NAG-ASN : bond 0.00327 ( 1) link_NAG-ASN : angle 1.18797 ( 3) hydrogen bonds : bond 0.02853 ( 73) hydrogen bonds : angle 6.27248 ( 183) SS BOND : bond 0.00206 ( 5) SS BOND : angle 0.46658 ( 10) covalent geometry : bond 0.00244 ( 2547) covalent geometry : angle 0.55198 ( 3466) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 620 Ramachandran restraints generated. 310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 620 Ramachandran restraints generated. 310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 71 time to evaluate : 0.294 Fit side-chains REVERT: C 417 LYS cc_start: 0.8508 (mmtp) cc_final: 0.8101 (mtpt) REVERT: C 462 LYS cc_start: 0.9098 (mtmt) cc_final: 0.8723 (mmtm) REVERT: H 19 ARG cc_start: 0.8009 (ttm-80) cc_final: 0.7467 (tpp80) REVERT: H 60 ASN cc_start: 0.9167 (t0) cc_final: 0.8819 (t0) REVERT: H 81 GLN cc_start: 0.8556 (tp40) cc_final: 0.7746 (tp40) outliers start: 5 outliers final: 5 residues processed: 73 average time/residue: 0.2205 time to fit residues: 18.1611 Evaluate side-chains 72 residues out of total 267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 67 time to evaluate : 0.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 486 PHE Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 98 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 28 optimal weight: 2.9990 chunk 21 optimal weight: 0.6980 chunk 9 optimal weight: 0.5980 chunk 11 optimal weight: 0.0980 chunk 13 optimal weight: 0.6980 chunk 2 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 chunk 27 optimal weight: 3.9990 chunk 8 optimal weight: 0.6980 chunk 5 optimal weight: 0.9990 chunk 16 optimal weight: 0.6980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 35 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 = 0.3537 r_free = 0.3537 target = 0.115651 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.099540 restraints weight = 4727.883| |-----------------------------------------------------------------------------| r_work (start): 0.3280 rms_B_bonded: 3.11 r_work: 0.3160 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3160 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 moved from start: 0.2840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 2553 Z= 0.138 Angle : 0.592 6.802 3479 Z= 0.292 Chirality : 0.044 0.127 371 Planarity : 0.004 0.034 447 Dihedral : 4.344 16.260 372 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 3.00 % Allowed : 17.23 % Favored : 79.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.91 (0.44), residues: 310 helix: -2.95 (0.91), residues: 26 sheet: 0.14 (0.51), residues: 96 loop : -0.62 (0.41), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 36 HIS 0.001 0.000 HIS H 53 PHE 0.009 0.001 PHE C 377 TYR 0.011 0.001 TYR H 79 ARG 0.006 0.001 ARG C 403 Details of bonding type rmsd link_NAG-ASN : bond 0.00267 ( 1) link_NAG-ASN : angle 1.27114 ( 3) hydrogen bonds : bond 0.02963 ( 73) hydrogen bonds : angle 6.23010 ( 183) SS BOND : bond 0.00159 ( 5) SS BOND : angle 0.42315 ( 10) covalent geometry : bond 0.00326 ( 2547) covalent geometry : angle 0.59125 ( 3466) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 620 Ramachandran restraints generated. 310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 620 Ramachandran restraints generated. 310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 68 time to evaluate : 0.268 Fit side-chains REVERT: C 417 LYS cc_start: 0.8475 (mmtp) cc_final: 0.8094 (mtpt) REVERT: C 462 LYS cc_start: 0.9111 (mtmt) cc_final: 0.8720 (mmtm) REVERT: H 19 ARG cc_start: 0.8067 (ttm-80) cc_final: 0.7454 (tpp80) REVERT: H 60 ASN cc_start: 0.9187 (t0) cc_final: 0.8823 (t0) REVERT: H 66 LEU cc_start: 0.8555 (mm) cc_final: 0.7843 (pp) REVERT: H 81 GLN cc_start: 0.8584 (tp40) cc_final: 0.7752 (tp40) outliers start: 8 outliers final: 8 residues processed: 71 average time/residue: 0.2053 time to fit residues: 16.5420 Evaluate side-chains 75 residues out of total 267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 67 time to evaluate : 0.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 486 PHE Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 54 ASP Chi-restraints excluded: chain H residue 98 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/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-5669/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/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-5669/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/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-5669/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-5669/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-5669/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-5669/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-5669/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-5669/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-5669/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-5669/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/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-5669/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-5669/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-5669/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-5669/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: 57.3801 > 50: distance: 63 - 120: 20.842 distance: 66 - 72: 16.601 distance: 72 - 73: 37.230 distance: 73 - 74: 34.011 distance: 74 - 75: 38.762 distance: 74 - 76: 41.057 distance: 76 - 77: 20.834 distance: 77 - 78: 15.366 distance: 77 - 80: 21.262 distance: 78 - 79: 43.994 distance: 78 - 83: 22.178 distance: 80 - 81: 12.140 distance: 80 - 82: 15.255 distance: 83 - 84: 25.293 distance: 84 - 85: 37.578 distance: 84 - 87: 20.653 distance: 85 - 86: 34.170 distance: 85 - 92: 26.889 distance: 87 - 88: 15.680 distance: 88 - 89: 14.177 distance: 89 - 90: 6.189 distance: 89 - 91: 14.751 distance: 92 - 93: 29.001 distance: 93 - 94: 24.380 distance: 94 - 95: 33.950 distance: 94 - 96: 39.276 distance: 96 - 97: 12.233 distance: 97 - 98: 9.381 distance: 97 - 100: 16.666 distance: 98 - 99: 27.565 distance: 98 - 107: 31.915 distance: 100 - 101: 13.305 distance: 101 - 102: 16.053 distance: 101 - 103: 15.351 distance: 102 - 104: 7.007 distance: 103 - 105: 12.875 distance: 104 - 106: 3.839 distance: 105 - 106: 6.095 distance: 107 - 108: 27.417 distance: 108 - 109: 21.628 distance: 108 - 111: 15.012 distance: 109 - 110: 52.331 distance: 109 - 115: 46.776 distance: 111 - 112: 18.465 distance: 112 - 113: 25.948 distance: 112 - 114: 21.975 distance: 115 - 116: 28.527 distance: 116 - 117: 19.608 distance: 116 - 119: 18.761 distance: 117 - 118: 34.312 distance: 117 - 121: 21.062 distance: 119 - 120: 30.045 distance: 121 - 122: 18.058 distance: 122 - 123: 16.096 distance: 122 - 125: 25.195 distance: 123 - 124: 49.806 distance: 123 - 133: 36.422 distance: 125 - 126: 30.391 distance: 126 - 127: 17.292 distance: 126 - 128: 19.638 distance: 127 - 129: 15.949 distance: 128 - 130: 4.306 distance: 129 - 131: 9.074 distance: 130 - 131: 6.953 distance: 131 - 132: 4.972 distance: 133 - 134: 25.002 distance: 134 - 135: 50.132 distance: 134 - 137: 43.622 distance: 135 - 136: 22.913 distance: 135 - 144: 19.332 distance: 137 - 138: 20.306 distance: 138 - 139: 5.021 distance: 138 - 140: 9.438 distance: 139 - 141: 19.329 distance: 140 - 142: 6.398 distance: 141 - 143: 17.027 distance: 142 - 143: 5.141 distance: 144 - 145: 35.627 distance: 144 - 150: 30.651 distance: 145 - 146: 35.118 distance: 145 - 148: 17.227 distance: 146 - 147: 57.380 distance: 146 - 151: 32.246 distance: 148 - 149: 23.288 distance: 149 - 150: 37.091