Starting phenix.real_space_refine on Sun Apr 27 02:51:38 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jln_61591/04_2025/9jln_61591.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jln_61591/04_2025/9jln_61591.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.84 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9jln_61591/04_2025/9jln_61591.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jln_61591/04_2025/9jln_61591.map" model { file = "/net/cci-nas-00/data/ceres_data/9jln_61591/04_2025/9jln_61591.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jln_61591/04_2025/9jln_61591.cif" } resolution = 2.84 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= -0.001 sd= 0.079 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: 6 Type Number sf(0) Gaussians S 33 5.16 5 Cl 1 4.86 5 Na 1 4.78 5 C 2898 2.51 5 N 629 2.21 5 O 733 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: 4295 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4139 Number of conformers: 1 Conformer: "" Number of residues, atoms: 521, 4139 Classifications: {'peptide': 521} Link IDs: {'PTRANS': 24, 'TRANS': 496} Chain: "A" Number of atoms: 156 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 156 Unusual residues: {' CL': 1, ' NA': 1, 'NAG': 3, 'TAU': 1, 'Y01': 3} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 3.47, per 1000 atoms: 0.81 Number of scatterers: 4295 At special positions: 0 Unit cell: (75.492, 71.764, 87.608, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Cl 1 17.00 S 33 16.00 Na 1 11.00 O 733 8.00 N 629 7.00 C 2898 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 162 " - pdb=" SG CYS A 171 " 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 A 701 " - " ASN A 163 " " NAG A 702 " - " ASN A 179 " " NAG A 703 " - " ASN A 190 " Time building additional restraints: 1.30 Conformation dependent library (CDL) restraints added in 570.4 milliseconds 1038 Ramachandran restraints generated. 519 Oldfield, 0 Emsley, 519 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 948 Finding SS restraints... Secondary structure from input PDB file: 33 helices and 0 sheets defined 82.9% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.36 Creating SS restraints... Processing helix chain 'A' and resid 47 through 59 removed outlier: 3.756A pdb=" N PHE A 58 " --> pdb=" O VAL A 54 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N VAL A 59 " --> pdb=" O ALA A 55 " (cutoff:3.500A) Processing helix chain 'A' and resid 60 through 65 removed outlier: 3.514A pdb=" N VAL A 64 " --> pdb=" O GLY A 60 " (cutoff:3.500A) Processing helix chain 'A' and resid 65 through 74 removed outlier: 3.765A pdb=" N TYR A 69 " --> pdb=" O TRP A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 76 through 78 No H-bonds generated for 'chain 'A' and resid 76 through 78' Processing helix chain 'A' and resid 79 through 106 removed outlier: 6.097A pdb=" N LEU A 92 " --> pdb=" O PHE A 88 " (cutoff:3.500A) Proline residue: A 93 - end of helix Processing helix chain 'A' and resid 109 through 117 removed outlier: 4.413A pdb=" N TRP A 113 " --> pdb=" O GLY A 109 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LYS A 115 " --> pdb=" O THR A 111 " (cutoff:3.500A) Processing helix chain 'A' and resid 118 through 120 No H-bonds generated for 'chain 'A' and resid 118 through 120' Processing helix chain 'A' and resid 121 through 153 removed outlier: 4.067A pdb=" N TYR A 125 " --> pdb=" O SER A 121 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N VAL A 136 " --> pdb=" O SER A 132 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N TYR A 137 " --> pdb=" O LEU A 133 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ILE A 139 " --> pdb=" O ASN A 135 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N VAL A 140 " --> pdb=" O VAL A 136 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N ILE A 141 " --> pdb=" O TYR A 137 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N LEU A 142 " --> pdb=" O TYR A 138 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N PHE A 153 " --> pdb=" O LEU A 149 " (cutoff:3.500A) Processing helix chain 'A' and resid 157 through 161 removed outlier: 3.933A pdb=" N HIS A 161 " --> pdb=" O PRO A 158 " (cutoff:3.500A) Processing helix chain 'A' and resid 173 through 177 Processing helix chain 'A' and resid 179 through 183 Processing helix chain 'A' and resid 193 through 202 Processing helix chain 'A' and resid 217 through 237 removed outlier: 3.623A pdb=" N ALA A 221 " --> pdb=" O LYS A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 244 through 266 removed outlier: 4.081A pdb=" N PHE A 248 " --> pdb=" O LYS A 244 " (cutoff:3.500A) Proline residue: A 253 - end of helix Processing helix chain 'A' and resid 269 through 279 removed outlier: 3.916A pdb=" N GLY A 273 " --> pdb=" O GLY A 269 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 286 Processing helix chain 'A' and resid 287 through 302 removed outlier: 4.316A pdb=" N TRP A 291 " --> pdb=" O ASP A 287 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N TYR A 302 " --> pdb=" O ILE A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 316 removed outlier: 3.823A pdb=" N ASN A 316 " --> pdb=" O LEU A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 321 through 356 removed outlier: 3.920A pdb=" N ASP A 325 " --> pdb=" O ASN A 321 " (cutoff:3.500A) Processing helix chain 'A' and resid 358 through 362 removed outlier: 3.836A pdb=" N VAL A 362 " --> pdb=" O ILE A 359 " (cutoff:3.500A) Processing helix chain 'A' and resid 366 through 368 No H-bonds generated for 'chain 'A' and resid 366 through 368' Processing helix chain 'A' and resid 369 through 378 Proline residue: A 375 - end of helix Processing helix chain 'A' and resid 383 through 418 removed outlier: 3.550A pdb=" N TRP A 387 " --> pdb=" O LEU A 383 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ASP A 401 " --> pdb=" O LEU A 397 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N SER A 402 " --> pdb=" O LEU A 398 " (cutoff:3.500A) Processing helix chain 'A' and resid 418 through 423 removed outlier: 4.194A pdb=" N LEU A 422 " --> pdb=" O TYR A 418 " (cutoff:3.500A) Processing helix chain 'A' and resid 426 through 444 removed outlier: 4.200A pdb=" N ILE A 430 " --> pdb=" O TYR A 426 " (cutoff:3.500A) removed outlier: 4.906A pdb=" N ILE A 432 " --> pdb=" O ARG A 428 " (cutoff:3.500A) Processing helix chain 'A' and resid 445 through 447 No H-bonds generated for 'chain 'A' and resid 445 through 447' Processing helix chain 'A' and resid 451 through 462 Processing helix chain 'A' and resid 465 through 482 removed outlier: 3.773A pdb=" N LEU A 469 " --> pdb=" O GLY A 465 " (cutoff:3.500A) Processing helix chain 'A' and resid 484 through 497 Processing helix chain 'A' and resid 503 through 510 Processing helix chain 'A' and resid 510 through 526 removed outlier: 3.713A pdb=" N VAL A 514 " --> pdb=" O VAL A 510 " (cutoff:3.500A) Processing helix chain 'A' and resid 539 through 555 removed outlier: 3.786A pdb=" N SER A 553 " --> pdb=" O LEU A 549 " (cutoff:3.500A) Processing helix chain 'A' and resid 555 through 567 267 hydrogen bonds defined for protein. 777 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: 1.20 Time building geometry restraints manager: 1.48 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 646 1.32 - 1.45: 1317 1.45 - 1.57: 2427 1.57 - 1.69: 0 1.69 - 1.82: 47 Bond restraints: 4437 Sorted by residual: bond pdb=" C1 NAG A 703 " pdb=" O5 NAG A 703 " ideal model delta sigma weight residual 1.406 1.476 -0.070 2.00e-02 2.50e+03 1.21e+01 bond pdb=" CAX Y01 A 706 " pdb=" OAF Y01 A 706 " ideal model delta sigma weight residual 1.247 1.308 -0.061 2.00e-02 2.50e+03 9.42e+00 bond pdb=" CAX Y01 A 708 " pdb=" OAF Y01 A 708 " ideal model delta sigma weight residual 1.247 1.307 -0.060 2.00e-02 2.50e+03 9.02e+00 bond pdb=" CAX Y01 A 707 " pdb=" OAH Y01 A 707 " ideal model delta sigma weight residual 1.248 1.308 -0.060 2.00e-02 2.50e+03 8.88e+00 bond pdb=" CAL Y01 A 706 " pdb=" CAX Y01 A 706 " ideal model delta sigma weight residual 1.540 1.501 0.039 2.00e-02 2.50e+03 3.76e+00 ... (remaining 4432 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.41: 5980 2.41 - 4.81: 75 4.81 - 7.21: 9 7.21 - 9.62: 3 9.62 - 12.02: 1 Bond angle restraints: 6068 Sorted by residual: angle pdb=" O1 TAU A 709 " pdb=" S TAU A 709 " pdb=" O2 TAU A 709 " ideal model delta sigma weight residual 113.04 101.02 12.02 3.00e+00 1.11e-01 1.61e+01 angle pdb=" C CYS A 556 " pdb=" N VAL A 557 " pdb=" CA VAL A 557 " ideal model delta sigma weight residual 120.33 122.78 -2.45 8.00e-01 1.56e+00 9.36e+00 angle pdb=" CA LEU A 555 " pdb=" CB LEU A 555 " pdb=" CG LEU A 555 " ideal model delta sigma weight residual 116.30 125.68 -9.38 3.50e+00 8.16e-02 7.19e+00 angle pdb=" CAL Y01 A 708 " pdb=" CAX Y01 A 708 " pdb=" OAH Y01 A 708 " ideal model delta sigma weight residual 115.62 123.15 -7.53 3.00e+00 1.11e-01 6.30e+00 angle pdb=" CAL Y01 A 706 " pdb=" CAX Y01 A 706 " pdb=" OAH Y01 A 706 " ideal model delta sigma weight residual 115.62 123.10 -7.48 3.00e+00 1.11e-01 6.22e+00 ... (remaining 6063 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.87: 2535 24.87 - 49.75: 120 49.75 - 74.62: 14 74.62 - 99.50: 9 99.50 - 124.37: 6 Dihedral angle restraints: 2684 sinusoidal: 1184 harmonic: 1500 Sorted by residual: dihedral pdb=" C2 NAG A 703 " pdb=" C1 NAG A 703 " pdb=" O5 NAG A 703 " pdb=" C5 NAG A 703 " ideal model delta sinusoidal sigma weight residual -62.96 61.41 -124.37 1 3.00e+01 1.11e-03 1.67e+01 dihedral pdb=" CAT Y01 A 707 " pdb=" CAR Y01 A 707 " pdb=" CBC Y01 A 707 " pdb=" OAW Y01 A 707 " ideal model delta sinusoidal sigma weight residual 178.96 60.45 118.51 1 3.00e+01 1.11e-03 1.58e+01 dihedral pdb=" CB CYS A 162 " pdb=" SG CYS A 162 " pdb=" SG CYS A 171 " pdb=" CB CYS A 171 " ideal model delta sinusoidal sigma weight residual -86.00 -119.29 33.29 1 1.00e+01 1.00e-02 1.58e+01 ... (remaining 2681 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 437 0.032 - 0.065: 169 0.065 - 0.097: 53 0.097 - 0.129: 22 0.129 - 0.161: 3 Chirality restraints: 684 Sorted by residual: chirality pdb=" CBB Y01 A 707 " pdb=" CAC Y01 A 707 " pdb=" CAO Y01 A 707 " pdb=" CBE Y01 A 707 " both_signs ideal model delta sigma weight residual False 2.58 2.41 0.16 2.00e-01 2.50e+01 6.52e-01 chirality pdb=" C1 NAG A 703 " pdb=" ND2 ASN A 190 " pdb=" C2 NAG A 703 " pdb=" O5 NAG A 703 " both_signs ideal model delta sigma weight residual False -2.40 -2.25 -0.15 2.00e-01 2.50e+01 5.29e-01 chirality pdb=" CBE Y01 A 707 " pdb=" CAP Y01 A 707 " pdb=" CBB Y01 A 707 " pdb=" CBI Y01 A 707 " both_signs ideal model delta sigma weight residual False 2.57 2.43 0.13 2.00e-01 2.50e+01 4.54e-01 ... (remaining 681 not shown) Planarity restraints: 720 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU A 87 " 0.009 2.00e-02 2.50e+03 1.77e-02 3.14e+00 pdb=" C LEU A 87 " -0.031 2.00e-02 2.50e+03 pdb=" O LEU A 87 " 0.012 2.00e-02 2.50e+03 pdb=" N PHE A 88 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU A 92 " 0.026 5.00e-02 4.00e+02 3.95e-02 2.49e+00 pdb=" N PRO A 93 " -0.068 5.00e-02 4.00e+02 pdb=" CA PRO A 93 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 93 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 478 " 0.007 2.00e-02 2.50e+03 1.41e-02 1.99e+00 pdb=" C VAL A 478 " -0.024 2.00e-02 2.50e+03 pdb=" O VAL A 478 " 0.009 2.00e-02 2.50e+03 pdb=" N ILE A 479 " 0.008 2.00e-02 2.50e+03 ... (remaining 717 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 625 2.76 - 3.29: 4243 3.29 - 3.83: 7070 3.83 - 4.36: 7781 4.36 - 4.90: 14146 Nonbonded interactions: 33865 Sorted by model distance: nonbonded pdb=" ND2 ASN A 63 " pdb=" OD1 ASN A 333 " model vdw 2.219 3.120 nonbonded pdb=" OG SER A 90 " pdb=" OG1 THR A 512 " model vdw 2.230 3.040 nonbonded pdb=" OH TYR A 69 " pdb=" OD2 ASP A 459 " model vdw 2.257 3.040 nonbonded pdb=" OAH Y01 A 707 " pdb=" OAH Y01 A 708 " model vdw 2.283 3.040 nonbonded pdb=" NE1 TRP A 65 " pdb=" O PRO A 367 " model vdw 2.303 3.120 ... (remaining 33860 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.740 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.190 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 15.420 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7245 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 : 0.004 0.070 4441 Z= 0.190 Angle : 0.657 12.025 6079 Z= 0.320 Chirality : 0.041 0.161 684 Planarity : 0.004 0.039 717 Dihedral : 16.025 124.369 1733 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 0.00 % Allowed : 0.22 % Favored : 99.78 % 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: 1.28 (0.39), residues: 519 helix: 1.69 (0.29), residues: 361 sheet: None (None), residues: 0 loop : -1.13 (0.52), residues: 158 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 470 HIS 0.002 0.000 HIS A 164 PHE 0.021 0.001 PHE A 338 TYR 0.017 0.001 TYR A 489 ARG 0.003 0.000 ARG A 428 Details of bonding type rmsd link_NAG-ASN : bond 0.00220 ( 3) link_NAG-ASN : angle 0.83903 ( 9) hydrogen bonds : bond 0.12643 ( 267) hydrogen bonds : angle 4.66527 ( 777) SS BOND : bond 0.00296 ( 1) SS BOND : angle 1.32831 ( 2) covalent geometry : bond 0.00378 ( 4437) covalent geometry : angle 0.65624 ( 6068) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1038 Ramachandran restraints generated. 519 Oldfield, 0 Emsley, 519 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1038 Ramachandran restraints generated. 519 Oldfield, 0 Emsley, 519 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 68 time to evaluate : 0.433 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 68 average time/residue: 0.9117 time to fit residues: 65.4977 Evaluate side-chains 55 residues out of total 445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 55 time to evaluate : 0.830 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 43 optimal weight: 0.0980 chunk 39 optimal weight: 4.9990 chunk 21 optimal weight: 0.8980 chunk 13 optimal weight: 0.5980 chunk 26 optimal weight: 3.9990 chunk 40 optimal weight: 2.9990 chunk 15 optimal weight: 0.9990 chunk 24 optimal weight: 0.9980 chunk 30 optimal weight: 0.7980 chunk 47 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 540 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4249 r_free = 0.4249 target = 0.175371 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.142553 restraints weight = 5285.585| |-----------------------------------------------------------------------------| r_work (start): 0.3900 rms_B_bonded: 2.35 r_work: 0.3771 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3771 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7448 moved from start: 0.1045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 4441 Z= 0.119 Angle : 0.596 11.300 6079 Z= 0.285 Chirality : 0.041 0.186 684 Planarity : 0.004 0.037 717 Dihedral : 13.119 112.468 842 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 1.57 % Allowed : 8.31 % Favored : 90.11 % 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: 1.29 (0.39), residues: 519 helix: 1.75 (0.28), residues: 365 sheet: None (None), residues: 0 loop : -1.38 (0.51), residues: 154 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 470 HIS 0.001 0.001 HIS A 164 PHE 0.014 0.001 PHE A 338 TYR 0.011 0.001 TYR A 69 ARG 0.007 0.001 ARG A 240 Details of bonding type rmsd link_NAG-ASN : bond 0.00215 ( 3) link_NAG-ASN : angle 1.47692 ( 9) hydrogen bonds : bond 0.04017 ( 267) hydrogen bonds : angle 4.13685 ( 777) SS BOND : bond 0.00280 ( 1) SS BOND : angle 0.98215 ( 2) covalent geometry : bond 0.00260 ( 4437) covalent geometry : angle 0.59376 ( 6068) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1038 Ramachandran restraints generated. 519 Oldfield, 0 Emsley, 519 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1038 Ramachandran restraints generated. 519 Oldfield, 0 Emsley, 519 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 60 time to evaluate : 0.480 Fit side-chains REVERT: A 133 LEU cc_start: 0.8063 (OUTLIER) cc_final: 0.7753 (mm) outliers start: 7 outliers final: 2 residues processed: 62 average time/residue: 0.9124 time to fit residues: 59.7651 Evaluate side-chains 58 residues out of total 445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 55 time to evaluate : 0.771 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain A residue 432 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- 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: 63.7152 > 50: distance: 18 - 23: 35.355 distance: 19 - 53: 28.921 distance: 23 - 24: 47.002 distance: 24 - 25: 51.714 distance: 24 - 27: 47.845 distance: 25 - 26: 24.743 distance: 25 - 30: 62.995 distance: 26 - 60: 11.790 distance: 27 - 28: 7.563 distance: 27 - 29: 39.950 distance: 30 - 31: 18.159 distance: 31 - 32: 42.039 distance: 31 - 34: 29.296 distance: 32 - 33: 54.506 distance: 32 - 42: 41.431 distance: 33 - 65: 23.104 distance: 34 - 35: 37.008 distance: 35 - 36: 32.653 distance: 35 - 37: 12.033 distance: 36 - 38: 27.983 distance: 37 - 39: 23.099 distance: 38 - 40: 33.159 distance: 39 - 40: 19.944 distance: 40 - 41: 21.670 distance: 42 - 43: 5.228 distance: 43 - 44: 41.027 distance: 43 - 46: 13.527 distance: 44 - 45: 56.936 distance: 44 - 53: 54.054 distance: 45 - 72: 34.155 distance: 46 - 47: 15.946 distance: 47 - 48: 18.496 distance: 47 - 49: 20.294 distance: 48 - 50: 52.204 distance: 49 - 51: 43.984 distance: 50 - 52: 39.162 distance: 51 - 52: 34.214 distance: 53 - 54: 41.816 distance: 54 - 55: 39.553 distance: 54 - 57: 14.374 distance: 55 - 56: 10.883 distance: 55 - 60: 29.932 distance: 57 - 58: 57.040 distance: 57 - 59: 34.186 distance: 60 - 61: 31.209 distance: 61 - 62: 40.996 distance: 62 - 63: 25.630 distance: 62 - 65: 56.683 distance: 65 - 66: 32.215 distance: 66 - 67: 38.776 distance: 66 - 69: 32.781 distance: 67 - 68: 18.118 distance: 67 - 72: 16.579 distance: 69 - 70: 43.985 distance: 69 - 71: 19.988 distance: 72 - 73: 5.556 distance: 73 - 74: 37.516 distance: 73 - 76: 58.450 distance: 74 - 75: 40.975 distance: 74 - 83: 34.603 distance: 75 - 106: 34.414 distance: 76 - 77: 52.262 distance: 77 - 78: 17.660 distance: 77 - 79: 24.797 distance: 78 - 80: 9.334 distance: 79 - 81: 12.056 distance: 80 - 82: 13.193 distance: 81 - 82: 9.433 distance: 83 - 84: 31.363 distance: 83 - 89: 13.760 distance: 84 - 85: 4.418 distance: 84 - 87: 28.826 distance: 85 - 86: 57.277 distance: 85 - 90: 9.566 distance: 86 - 113: 25.857 distance: 87 - 88: 49.413 distance: 88 - 89: 21.207 distance: 90 - 91: 54.154 distance: 91 - 92: 33.648 distance: 91 - 94: 40.592 distance: 93 - 120: 35.363 distance: 94 - 95: 28.236 distance: 95 - 96: 27.625 distance: 95 - 97: 36.122 distance: 96 - 98: 23.129 distance: 97 - 99: 34.335 distance: 98 - 100: 26.101 distance: 99 - 100: 27.572 distance: 101 - 102: 10.343 distance: 102 - 103: 42.959 distance: 102 - 105: 32.378 distance: 103 - 104: 18.955 distance: 103 - 106: 20.052 distance: 104 - 127: 29.111