Starting phenix.real_space_refine on Fri Dec 8 04:16:50 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t1j_40969/12_2023/8t1j_40969_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t1j_40969/12_2023/8t1j_40969.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t1j_40969/12_2023/8t1j_40969.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t1j_40969/12_2023/8t1j_40969.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t1j_40969/12_2023/8t1j_40969_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t1j_40969/12_2023/8t1j_40969_updated.pdb" } resolution = 2.7 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= 0.121 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 Fe 2 7.16 5 Zn 1 6.06 5 S 42 5.16 5 C 4460 2.51 5 N 1202 2.21 5 O 1266 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 299": "NH1" <-> "NH2" Residue "A ARG 343": "NH1" <-> "NH2" Residue "A ARG 349": "NH1" <-> "NH2" Residue "A ARG 371": "NH1" <-> "NH2" Residue "A ARG 380": "NH1" <-> "NH2" Residue "A ARG 410": "NH1" <-> "NH2" Residue "A ARG 414": "NH1" <-> "NH2" Residue "A ARG 418": "NH1" <-> "NH2" Residue "A ARG 430": "NH1" <-> "NH2" Residue "A ARG 456": "NH1" <-> "NH2" Residue "A ARG 465": "NH1" <-> "NH2" Residue "A ARG 473": "NH1" <-> "NH2" Residue "A ARG 481": "NH1" <-> "NH2" Residue "A ARG 514": "NH1" <-> "NH2" Residue "A ARG 516": "NH1" <-> "NH2" Residue "A ARG 547": "NH1" <-> "NH2" Residue "A ARG 596": "NH1" <-> "NH2" Residue "A ARG 603": "NH1" <-> "NH2" Residue "A ARG 619": "NH1" <-> "NH2" Residue "A ARG 667": "NH1" <-> "NH2" Residue "A ARG 669": "NH1" <-> "NH2" Residue "A TYR 698": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 699": "NH1" <-> "NH2" Residue "B ARG 299": "NH1" <-> "NH2" Residue "B ARG 343": "NH1" <-> "NH2" Residue "B ARG 349": "NH1" <-> "NH2" Residue "B ARG 371": "NH1" <-> "NH2" Residue "B ARG 380": "NH1" <-> "NH2" Residue "B ARG 410": "NH1" <-> "NH2" Residue "B ARG 414": "NH1" <-> "NH2" Residue "B ARG 418": "NH1" <-> "NH2" Residue "B ARG 430": "NH1" <-> "NH2" Residue "B ARG 456": "NH1" <-> "NH2" Residue "B ARG 465": "NH1" <-> "NH2" Residue "B ARG 473": "NH1" <-> "NH2" Residue "B ARG 481": "NH1" <-> "NH2" Residue "B ARG 514": "NH1" <-> "NH2" Residue "B ARG 516": "NH1" <-> "NH2" Residue "B ARG 547": "NH1" <-> "NH2" Residue "B TYR 562": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 596": "NH1" <-> "NH2" Residue "B ARG 603": "NH1" <-> "NH2" Residue "B ARG 619": "NH1" <-> "NH2" Residue "B ARG 667": "NH1" <-> "NH2" Residue "B ARG 669": "NH1" <-> "NH2" Residue "B ARG 699": "NH1" <-> "NH2" Residue "A ARG 1502": "NH1" <-> "NH2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 6973 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 3414 Number of conformers: 1 Conformer: "" Number of residues, atoms: 419, 3414 Classifications: {'peptide': 419} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 396} Chain: "B" Number of atoms: 3414 Number of conformers: 1 Conformer: "" Number of residues, atoms: 419, 3414 Classifications: {'peptide': 419} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 396} Chain: "A" Number of atoms: 73 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 73 Unusual residues: {' ZN': 1, 'H4B': 1, 'HEM': 1} Inner-chain residues flagged as termini: ['pdbres="ARG A1502 "'] Classifications: {'peptide': 1, 'undetermined': 3} Modifications used: {'COO': 1} Link IDs: {None: 3} Chain: "B" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 12 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "B" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 60 Unusual residues: {'H4B': 1, 'HEM': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 234 SG CYS A 326 33.487 54.832 48.590 1.00 0.00 S ATOM 274 SG CYS A 331 33.594 52.036 51.805 1.00 0.00 S ATOM 3648 SG CYS B 326 36.099 54.944 52.568 1.00 0.00 S ATOM 3688 SG CYS B 331 36.316 52.165 49.106 1.00 0.00 S ATOM 965 SG CYS A 415 42.977 42.732 34.962 1.00 0.00 S ATOM 4379 SG CYS B 415 28.567 40.706 65.373 1.00 0.00 S Time building chain proxies: 3.94, per 1000 atoms: 0.57 Number of scatterers: 6973 At special positions: 0 Unit cell: (74.13, 83.661, 101.664, 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) Zn 1 29.99 Fe 2 26.01 S 42 16.00 O 1266 8.00 N 1202 7.00 C 4460 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.76 Conformation dependent library (CDL) restraints added in 1.2 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1501 " pdb="ZN ZN A1501 " - pdb=" SG CYS A 331 " pdb="ZN ZN A1501 " - pdb=" SG CYS B 331 " pdb="ZN ZN A1501 " - pdb=" SG CYS A 326 " pdb="ZN ZN A1501 " - pdb=" SG CYS B 326 " Number of angles added : 6 1668 Ramachandran restraints generated. 834 Oldfield, 0 Emsley, 834 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1584 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 36 helices and 12 sheets defined 38.1% alpha, 8.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.47 Creating SS restraints... Processing helix chain 'A' and resid 316 through 319 Processing helix chain 'A' and resid 351 through 368 Proline residue: A 356 - end of helix Processing helix chain 'A' and resid 375 through 391 Processing helix chain 'A' and resid 398 through 410 Processing helix chain 'A' and resid 418 through 420 No H-bonds generated for 'chain 'A' and resid 418 through 420' Processing helix chain 'A' and resid 435 through 453 removed outlier: 6.379A pdb=" N LYS A 452 " --> pdb=" O TYR A 448 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N GLY A 453 " --> pdb=" O ALA A 449 " (cutoff:3.500A) Processing helix chain 'A' and resid 496 through 508 removed outlier: 5.333A pdb=" N GLN A 500 " --> pdb=" O ALA A 497 " (cutoff:3.500A) Processing helix chain 'A' and resid 538 through 540 No H-bonds generated for 'chain 'A' and resid 538 through 540' Processing helix chain 'A' and resid 554 through 557 Processing helix chain 'A' and resid 590 through 594 Processing helix chain 'A' and resid 607 through 613 Processing helix chain 'A' and resid 621 through 623 No H-bonds generated for 'chain 'A' and resid 621 through 623' Processing helix chain 'A' and resid 625 through 643 Processing helix chain 'A' and resid 651 through 668 Processing helix chain 'A' and resid 676 through 679 No H-bonds generated for 'chain 'A' and resid 676 through 679' Processing helix chain 'A' and resid 685 through 687 No H-bonds generated for 'chain 'A' and resid 685 through 687' Processing helix chain 'A' and resid 689 through 692 removed outlier: 3.627A pdb=" N HIS A 692 " --> pdb=" O PRO A 689 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 689 through 692' Processing helix chain 'A' and resid 710 through 712 No H-bonds generated for 'chain 'A' and resid 710 through 712' Processing helix chain 'B' and resid 316 through 319 Processing helix chain 'B' and resid 351 through 368 Proline residue: B 356 - end of helix Processing helix chain 'B' and resid 375 through 391 Processing helix chain 'B' and resid 398 through 410 Processing helix chain 'B' and resid 418 through 420 No H-bonds generated for 'chain 'B' and resid 418 through 420' Processing helix chain 'B' and resid 435 through 453 removed outlier: 6.392A pdb=" N LYS B 452 " --> pdb=" O TYR B 448 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N GLY B 453 " --> pdb=" O ALA B 449 " (cutoff:3.500A) Processing helix chain 'B' and resid 496 through 508 removed outlier: 3.502A pdb=" N VAL B 499 " --> pdb=" O PRO B 496 " (cutoff:3.500A) removed outlier: 5.320A pdb=" N GLN B 500 " --> pdb=" O ALA B 497 " (cutoff:3.500A) Processing helix chain 'B' and resid 538 through 540 No H-bonds generated for 'chain 'B' and resid 538 through 540' Processing helix chain 'B' and resid 554 through 557 Processing helix chain 'B' and resid 590 through 594 Processing helix chain 'B' and resid 607 through 613 Processing helix chain 'B' and resid 621 through 623 No H-bonds generated for 'chain 'B' and resid 621 through 623' Processing helix chain 'B' and resid 625 through 643 Processing helix chain 'B' and resid 651 through 668 Processing helix chain 'B' and resid 676 through 679 No H-bonds generated for 'chain 'B' and resid 676 through 679' Processing helix chain 'B' and resid 685 through 687 No H-bonds generated for 'chain 'B' and resid 685 through 687' Processing helix chain 'B' and resid 689 through 692 Processing helix chain 'B' and resid 710 through 712 No H-bonds generated for 'chain 'B' and resid 710 through 712' Processing sheet with id= A, first strand: chain 'A' and resid 301 through 304 Processing sheet with id= B, first strand: chain 'A' and resid 425 through 429 Processing sheet with id= C, first strand: chain 'A' and resid 484 through 486 Processing sheet with id= D, first strand: chain 'A' and resid 522 through 524 Processing sheet with id= E, first strand: chain 'A' and resid 543 through 545 Processing sheet with id= F, first strand: chain 'A' and resid 703 through 706 Processing sheet with id= G, first strand: chain 'B' and resid 301 through 304 Processing sheet with id= H, first strand: chain 'B' and resid 425 through 429 Processing sheet with id= I, first strand: chain 'B' and resid 484 through 486 Processing sheet with id= J, first strand: chain 'B' and resid 522 through 524 Processing sheet with id= K, first strand: chain 'B' and resid 543 through 545 Processing sheet with id= L, first strand: chain 'B' and resid 703 through 706 228 hydrogen bonds defined for protein. 588 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: 1.81 Time building geometry restraints manager: 2.91 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.40: 2923 1.40 - 1.59: 4185 1.59 - 1.78: 2 1.78 - 1.98: 65 1.98 - 2.17: 5 Bond restraints: 7180 Sorted by residual: bond pdb=" C3B HEM B1503 " pdb=" CAB HEM B1503 " ideal model delta sigma weight residual 1.544 1.391 0.153 2.00e-02 2.50e+03 5.81e+01 bond pdb=" C3B HEM A1504 " pdb=" CAB HEM A1504 " ideal model delta sigma weight residual 1.544 1.394 0.150 2.00e-02 2.50e+03 5.60e+01 bond pdb=" C3C HEM B1503 " pdb=" CAC HEM B1503 " ideal model delta sigma weight residual 1.544 1.402 0.142 2.00e-02 2.50e+03 5.03e+01 bond pdb=" C3C HEM A1504 " pdb=" CAC HEM A1504 " ideal model delta sigma weight residual 1.544 1.409 0.135 2.00e-02 2.50e+03 4.57e+01 bond pdb=" C4A H4B A1503 " pdb=" N5 H4B A1503 " ideal model delta sigma weight residual 1.368 1.465 -0.097 1.60e-02 3.91e+03 3.68e+01 ... (remaining 7175 not shown) Histogram of bond angle deviations from ideal: 87.27 - 102.91: 85 102.91 - 118.55: 5664 118.55 - 134.19: 4017 134.19 - 149.83: 0 149.83 - 165.47: 4 Bond angle restraints: 9770 Sorted by residual: angle pdb=" N LEU A 354 " pdb=" CA LEU A 354 " pdb=" C LEU A 354 " ideal model delta sigma weight residual 111.36 119.13 -7.77 1.09e+00 8.42e-01 5.08e+01 angle pdb=" N LEU B 354 " pdb=" CA LEU B 354 " pdb=" C LEU B 354 " ideal model delta sigma weight residual 111.36 119.12 -7.76 1.09e+00 8.42e-01 5.07e+01 angle pdb=" N VAL B 499 " pdb=" CA VAL B 499 " pdb=" C VAL B 499 " ideal model delta sigma weight residual 110.42 116.18 -5.76 9.60e-01 1.09e+00 3.59e+01 angle pdb=" N1 H4B B1502 " pdb=" C2 H4B B1502 " pdb=" N3 H4B B1502 " ideal model delta sigma weight residual 123.14 117.15 5.99 1.00e+00 1.00e+00 3.59e+01 angle pdb=" N ASN A 712 " pdb=" CA ASN A 712 " pdb=" C ASN A 712 " ideal model delta sigma weight residual 113.17 105.66 7.51 1.26e+00 6.30e-01 3.55e+01 ... (remaining 9765 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.64: 4088 21.64 - 43.28: 95 43.28 - 64.92: 29 64.92 - 86.56: 10 86.56 - 108.20: 8 Dihedral angle restraints: 4230 sinusoidal: 1778 harmonic: 2452 Sorted by residual: dihedral pdb=" C2B HEM A1504 " pdb=" C3B HEM A1504 " pdb=" CAB HEM A1504 " pdb=" CBB HEM A1504 " ideal model delta sinusoidal sigma weight residual 180.00 -101.42 -78.58 2 1.00e+01 1.00e-02 4.61e+01 dihedral pdb=" C2B HEM B1503 " pdb=" C3B HEM B1503 " pdb=" CAB HEM B1503 " pdb=" CBB HEM B1503 " ideal model delta sinusoidal sigma weight residual -180.00 -118.80 -61.20 2 1.00e+01 1.00e-02 3.69e+01 dihedral pdb=" CA TYR A 588 " pdb=" C TYR A 588 " pdb=" N MET A 589 " pdb=" CA MET A 589 " ideal model delta harmonic sigma weight residual 180.00 151.45 28.55 0 5.00e+00 4.00e-02 3.26e+01 ... (remaining 4227 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.070: 676 0.070 - 0.139: 265 0.139 - 0.209: 56 0.209 - 0.278: 15 0.278 - 0.348: 2 Chirality restraints: 1014 Sorted by residual: chirality pdb=" CA VAL B 474 " pdb=" N VAL B 474 " pdb=" C VAL B 474 " pdb=" CB VAL B 474 " both_signs ideal model delta sigma weight residual False 2.44 2.79 -0.35 2.00e-01 2.50e+01 3.02e+00 chirality pdb=" CA ASP B 471 " pdb=" N ASP B 471 " pdb=" C ASP B 471 " pdb=" CB ASP B 471 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.78e+00 chirality pdb=" CA ASP B 347 " pdb=" N ASP B 347 " pdb=" C ASP B 347 " pdb=" CB ASP B 347 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.26 2.00e-01 2.50e+01 1.63e+00 ... (remaining 1011 not shown) Planarity restraints: 1240 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1A HEM A1504 " 0.015 2.00e-02 2.50e+03 1.26e-01 3.55e+02 pdb=" C2A HEM A1504 " 0.038 2.00e-02 2.50e+03 pdb=" C3A HEM A1504 " 0.104 2.00e-02 2.50e+03 pdb=" C4A HEM A1504 " 0.015 2.00e-02 2.50e+03 pdb=" CAA HEM A1504 " -0.251 2.00e-02 2.50e+03 pdb=" CHA HEM A1504 " 0.100 2.00e-02 2.50e+03 pdb=" CHB HEM A1504 " -0.174 2.00e-02 2.50e+03 pdb=" CMA HEM A1504 " 0.162 2.00e-02 2.50e+03 pdb=" NA HEM A1504 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" ND HEM B1503 " -0.136 2.00e-02 2.50e+03 1.08e-01 2.62e+02 pdb=" C1D HEM B1503 " -0.147 2.00e-02 2.50e+03 pdb=" C2D HEM B1503 " -0.080 2.00e-02 2.50e+03 pdb=" C3D HEM B1503 " -0.024 2.00e-02 2.50e+03 pdb=" C4D HEM B1503 " -0.002 2.00e-02 2.50e+03 pdb=" CAD HEM B1503 " -0.003 2.00e-02 2.50e+03 pdb=" CHA HEM B1503 " 0.145 2.00e-02 2.50e+03 pdb=" CHD HEM B1503 " 0.179 2.00e-02 2.50e+03 pdb=" CMD HEM B1503 " 0.068 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" NB HEM A1504 " 0.164 2.00e-02 2.50e+03 1.01e-01 2.28e+02 pdb=" C1B HEM A1504 " 0.019 2.00e-02 2.50e+03 pdb=" C2B HEM A1504 " -0.013 2.00e-02 2.50e+03 pdb=" C3B HEM A1504 " -0.003 2.00e-02 2.50e+03 pdb=" C4B HEM A1504 " 0.071 2.00e-02 2.50e+03 pdb=" CAB HEM A1504 " -0.092 2.00e-02 2.50e+03 pdb=" CHB HEM A1504 " -0.181 2.00e-02 2.50e+03 pdb=" CHC HEM A1504 " -0.074 2.00e-02 2.50e+03 pdb=" CMB HEM A1504 " 0.108 2.00e-02 2.50e+03 ... (remaining 1237 not shown) Histogram of nonbonded interaction distances: 2.50 - 2.98: 3435 2.98 - 3.46: 6759 3.46 - 3.94: 12183 3.94 - 4.42: 14745 4.42 - 4.90: 22161 Nonbonded interactions: 59283 Sorted by model distance: nonbonded pdb=" N ASN B 712 " pdb=" N THR B 713 " model vdw 2.502 2.560 nonbonded pdb=" N ASN A 712 " pdb=" N THR A 713 " model vdw 2.502 2.560 nonbonded pdb=" O THR B 433 " pdb=" ND2 ASN B 527 " model vdw 2.525 2.520 nonbonded pdb=" OE1 GLN B 478 " pdb=" NH1 ARG B 481 " model vdw 2.526 2.520 nonbonded pdb=" O THR A 433 " pdb=" ND2 ASN A 527 " model vdw 2.531 2.520 ... (remaining 59278 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 298 through 716 or resid 1502 through 1504)) selection = chain 'B' } 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: 1.720 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: 7.280 Check model and map are aligned: 0.100 Set scattering table: 0.070 Process input model: 22.810 Find NCS groups from input model: 0.410 Set up NCS constraints: 0.040 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: 0.010 Load rotamer database and sin/cos tables:12.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7553 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 : 0.012 0.156 7180 Z= 0.772 Angle : 1.447 26.910 9770 Z= 0.969 Chirality : 0.075 0.348 1014 Planarity : 0.011 0.126 1240 Dihedral : 12.837 108.198 2646 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 0.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 0.00 % Allowed : 0.53 % Favored : 99.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 0.15 (0.26), residues: 834 helix: -0.01 (0.26), residues: 296 sheet: 0.14 (0.56), residues: 78 loop : 0.33 (0.27), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.065 0.006 TRP B 711 HIS 0.009 0.001 HIS B 714 PHE 0.035 0.003 PHE B 554 TYR 0.100 0.016 TYR A 604 ARG 0.008 0.001 ARG B 414 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1668 Ramachandran restraints generated. 834 Oldfield, 0 Emsley, 834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1668 Ramachandran restraints generated. 834 Oldfield, 0 Emsley, 834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 144 time to evaluate : 0.858 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 144 average time/residue: 1.5205 time to fit residues: 228.1076 Evaluate side-chains 83 residues out of total 752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 83 time to evaluate : 0.813 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.0948 ------------------------------------------------------------------------------- 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: 1.9990 chunk 62 optimal weight: 0.9990 chunk 34 optimal weight: 0.9980 chunk 21 optimal weight: 0.6980 chunk 41 optimal weight: 0.9990 chunk 33 optimal weight: 0.5980 chunk 64 optimal weight: 1.9990 chunk 24 optimal weight: 0.9990 chunk 39 optimal weight: 0.6980 chunk 47 optimal weight: 0.5980 chunk 74 optimal weight: 0.5980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 364 GLN A 445 HIS A 525 GLN A 535 GLN B 353 GLN B 385 ASN B 642 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7695 moved from start: 0.2475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 7180 Z= 0.219 Angle : 0.628 17.021 9770 Z= 0.293 Chirality : 0.042 0.135 1014 Planarity : 0.004 0.036 1240 Dihedral : 11.238 99.521 962 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 2.13 % Allowed : 9.18 % Favored : 88.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 1.26 (0.28), residues: 834 helix: 1.34 (0.30), residues: 302 sheet: 0.03 (0.59), residues: 76 loop : 0.82 (0.29), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 587 HIS 0.017 0.001 HIS B 714 PHE 0.014 0.002 PHE B 300 TYR 0.012 0.001 TYR A 366 ARG 0.004 0.000 ARG A 414 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1668 Ramachandran restraints generated. 834 Oldfield, 0 Emsley, 834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1668 Ramachandran restraints generated. 834 Oldfield, 0 Emsley, 834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 88 time to evaluate : 0.801 Fit side-chains outliers start: 16 outliers final: 8 residues processed: 97 average time/residue: 1.6094 time to fit residues: 163.1021 Evaluate side-chains 82 residues out of total 752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 74 time to evaluate : 0.808 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 6 residues processed: 2 average time/residue: 1.3878 time to fit residues: 3.9958 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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-1.21rc1-5172/modules/cctbx_project/iotbx/cli_parser.py", line 931, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/programs/real_space_refine.py", line 191, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 297, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 673, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 737, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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-1.21rc1-5172/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-1.21rc1-5172/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-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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-1.21rc1-5172/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-1.21rc1-5172/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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-1.21rc1-5172/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-1.21rc1-5172/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 66.6408 > 50: distance: 10 - 15: 35.338 distance: 15 - 16: 48.243 distance: 16 - 17: 29.730 distance: 16 - 19: 21.536 distance: 17 - 18: 27.358 distance: 17 - 26: 51.430 distance: 19 - 20: 18.198 distance: 20 - 21: 49.616 distance: 21 - 22: 6.865 distance: 22 - 23: 6.866 distance: 23 - 24: 3.344 distance: 26 - 27: 30.203 distance: 27 - 28: 26.846 distance: 27 - 30: 26.764 distance: 28 - 29: 39.706 distance: 28 - 36: 19.576 distance: 30 - 31: 21.935 distance: 31 - 32: 26.539 distance: 31 - 33: 15.560 distance: 33 - 35: 9.354 distance: 36 - 37: 18.131 distance: 36 - 42: 11.014 distance: 37 - 38: 43.808 distance: 37 - 40: 53.553 distance: 38 - 39: 39.467 distance: 38 - 43: 35.301 distance: 40 - 41: 23.594 distance: 41 - 42: 33.782 distance: 43 - 44: 30.863 distance: 44 - 45: 7.246 distance: 44 - 47: 22.550 distance: 45 - 46: 8.969 distance: 45 - 52: 33.169 distance: 47 - 48: 17.035 distance: 48 - 49: 7.532 distance: 49 - 50: 16.104 distance: 50 - 51: 15.676 distance: 52 - 53: 7.736 distance: 53 - 54: 43.454 distance: 53 - 56: 31.799 distance: 54 - 55: 13.839 distance: 54 - 63: 32.734 distance: 56 - 57: 14.664 distance: 57 - 58: 9.365 distance: 57 - 59: 15.421 distance: 58 - 60: 31.749 distance: 59 - 61: 15.636 distance: 60 - 62: 17.873 distance: 61 - 62: 28.285 distance: 63 - 64: 27.603 distance: 64 - 65: 18.569 distance: 64 - 67: 21.877 distance: 65 - 71: 56.025 distance: 67 - 68: 54.028 distance: 68 - 69: 23.424 distance: 68 - 70: 34.506 distance: 71 - 72: 15.457 distance: 72 - 73: 24.470 distance: 72 - 75: 48.391 distance: 73 - 85: 58.933 distance: 75 - 76: 44.356 distance: 76 - 77: 36.634 distance: 76 - 78: 45.786 distance: 77 - 79: 35.549 distance: 78 - 80: 38.020 distance: 78 - 81: 38.423 distance: 79 - 80: 20.644 distance: 80 - 82: 20.645 distance: 81 - 83: 64.226 distance: 82 - 84: 23.874 distance: 83 - 84: 44.036 distance: 85 - 86: 42.633 distance: 86 - 89: 64.297 distance: 87 - 96: 50.573 distance: 88 - 113: 36.422 distance: 89 - 90: 12.303 distance: 90 - 91: 43.828 distance: 90 - 92: 14.635 distance: 91 - 93: 15.532 distance: 92 - 94: 39.139 distance: 93 - 95: 14.462 distance: 94 - 95: 21.686 distance: 96 - 97: 14.314 distance: 97 - 98: 19.621 distance: 97 - 100: 31.607 distance: 98 - 99: 51.927 distance: 98 - 105: 33.870 distance: 100 - 101: 30.695 distance: 101 - 102: 39.246 distance: 103 - 104: 42.685 distance: 105 - 106: 4.232 distance: 106 - 107: 12.833 distance: 106 - 109: 13.055 distance: 107 - 108: 49.685 distance: 107 - 113: 34.680 distance: 109 - 110: 11.635 distance: 110 - 111: 21.544 distance: 110 - 112: 49.051 distance: 144 - 159: 3.373 distance: 162 - 173: 3.150