Starting phenix.real_space_refine on Fri Aug 2 14:17:52 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n5g_24189/08_2024/7n5g_24189.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n5g_24189/08_2024/7n5g_24189.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n5g_24189/08_2024/7n5g_24189.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n5g_24189/08_2024/7n5g_24189.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n5g_24189/08_2024/7n5g_24189.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n5g_24189/08_2024/7n5g_24189.cif" } resolution = 2.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.023 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 12 5.16 5 C 1920 2.51 5 N 486 2.21 5 O 508 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B PHE 335": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 512": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 574": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 589": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 642": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 654": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 715": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 2926 Number of models: 1 Model: "" Number of chains: 2 Chain: "B" Number of atoms: 2908 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2908 Classifications: {'peptide': 371} Incomplete info: {'truncation_to_alanine': 37} Link IDs: {'PTRANS': 7, 'TRANS': 363} Chain breaks: 4 Unresolved non-hydrogen bonds: 128 Unresolved non-hydrogen angles: 170 Unresolved non-hydrogen dihedrals: 110 Unresolved non-hydrogen chiralities: 21 Planarities with less than four sites: {'PHE:plan': 3, 'GLU:plan': 1, 'TRP:plan': 2, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 50 Chain: "B" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 18 Unusual residues: {'PLM': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.84, per 1000 atoms: 0.97 Number of scatterers: 2926 At special positions: 0 Unit cell: (70.04, 93.73, 140.08, 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 12 16.00 O 508 8.00 N 486 7.00 C 1920 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=0, symmetry=0 Time building additional restraints: 1.00 Conformation dependent library (CDL) restraints added in 665.4 milliseconds 722 Ramachandran restraints generated. 361 Oldfield, 0 Emsley, 361 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 720 Finding SS restraints... Secondary structure from input PDB file: 14 helices and 2 sheets defined 63.9% alpha, 11.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.33 Creating SS restraints... Processing helix chain 'B' and resid 186 through 203 Processing helix chain 'B' and resid 223 through 232 Processing helix chain 'B' and resid 235 through 241 Processing helix chain 'B' and resid 265 through 285 Processing helix chain 'B' and resid 295 through 329 removed outlier: 3.824A pdb=" N LEU B 299 " --> pdb=" O THR B 295 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N SER B 329 " --> pdb=" O ILE B 325 " (cutoff:3.500A) Processing helix chain 'B' and resid 330 through 331 No H-bonds generated for 'chain 'B' and resid 330 through 331' Processing helix chain 'B' and resid 332 through 334 No H-bonds generated for 'chain 'B' and resid 332 through 334' Processing helix chain 'B' and resid 335 through 349 Processing helix chain 'B' and resid 508 through 524 Processing helix chain 'B' and resid 526 through 552 Processing helix chain 'B' and resid 556 through 590 removed outlier: 5.467A pdb=" N ASN B 576 " --> pdb=" O PHE B 572 " (cutoff:3.500A) removed outlier: 5.843A pdb=" N THR B 577 " --> pdb=" O ILE B 573 " (cutoff:3.500A) Processing helix chain 'B' and resid 631 through 635 Processing helix chain 'B' and resid 661 through 678 Processing helix chain 'B' and resid 714 through 737 Processing sheet with id=AA1, first strand: chain 'B' and resid 626 through 630 removed outlier: 7.157A pdb=" N THR B 616 " --> pdb=" O MET B 612 " (cutoff:3.500A) removed outlier: 5.243A pdb=" N MET B 612 " --> pdb=" O THR B 616 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N VAL B 618 " --> pdb=" O GLU B 610 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 649 through 657 removed outlier: 6.485A pdb=" N LYS B 699 " --> pdb=" O ILE B 694 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N ILE B 694 " --> pdb=" O LYS B 699 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N LYS B 701 " --> pdb=" O LYS B 692 " (cutoff:3.500A) 206 hydrogen bonds defined for protein. 612 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: 0.78 Time building geometry restraints manager: 1.12 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: 675 1.32 - 1.44: 718 1.44 - 1.57: 1550 1.57 - 1.69: 16 1.69 - 1.81: 21 Bond restraints: 2980 Sorted by residual: bond pdb=" CD2 TRP B 507 " pdb=" CE3 TRP B 507 " ideal model delta sigma weight residual 1.398 1.503 -0.105 1.60e-02 3.91e+03 4.27e+01 bond pdb=" CZ2 TRP B 507 " pdb=" CH2 TRP B 507 " ideal model delta sigma weight residual 1.368 1.480 -0.112 1.90e-02 2.77e+03 3.46e+01 bond pdb=" CB ILE B 285 " pdb=" CG1 ILE B 285 " ideal model delta sigma weight residual 1.530 1.635 -0.105 2.00e-02 2.50e+03 2.77e+01 bond pdb=" CB TYR B 629 " pdb=" CG TYR B 629 " ideal model delta sigma weight residual 1.512 1.399 0.113 2.20e-02 2.07e+03 2.65e+01 bond pdb=" CB HIS B 345 " pdb=" CG HIS B 345 " ideal model delta sigma weight residual 1.497 1.428 0.069 1.40e-02 5.10e+03 2.46e+01 ... (remaining 2975 not shown) Histogram of bond angle deviations from ideal: 98.83 - 105.94: 53 105.94 - 113.05: 1626 113.05 - 120.16: 1256 120.16 - 127.27: 1072 127.27 - 134.38: 32 Bond angle restraints: 4039 Sorted by residual: angle pdb=" C HIS B 592 " pdb=" N PRO B 593 " pdb=" CA PRO B 593 " ideal model delta sigma weight residual 119.56 126.54 -6.98 1.01e+00 9.80e-01 4.78e+01 angle pdb=" C SER B 645 " pdb=" N PRO B 646 " pdb=" CA PRO B 646 " ideal model delta sigma weight residual 120.52 126.91 -6.39 9.90e-01 1.02e+00 4.17e+01 angle pdb=" C LEU B 743 " pdb=" N PRO B 744 " pdb=" CA PRO B 744 " ideal model delta sigma weight residual 119.85 126.24 -6.39 1.01e+00 9.80e-01 4.00e+01 angle pdb=" C GLN B 291 " pdb=" N PRO B 292 " pdb=" CA PRO B 292 " ideal model delta sigma weight residual 119.28 125.41 -6.13 1.10e+00 8.26e-01 3.11e+01 angle pdb=" N SER B 267 " pdb=" CA SER B 267 " pdb=" C SER B 267 " ideal model delta sigma weight residual 112.23 105.58 6.65 1.26e+00 6.30e-01 2.79e+01 ... (remaining 4034 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.33: 1685 14.33 - 28.65: 62 28.65 - 42.97: 7 42.97 - 57.30: 11 57.30 - 71.62: 6 Dihedral angle restraints: 1771 sinusoidal: 680 harmonic: 1091 Sorted by residual: dihedral pdb=" CA ASP B 657 " pdb=" CB ASP B 657 " pdb=" CG ASP B 657 " pdb=" OD1 ASP B 657 " ideal model delta sinusoidal sigma weight residual -30.00 -84.87 54.87 1 2.00e+01 2.50e-03 1.02e+01 dihedral pdb=" CA ASP B 595 " pdb=" CB ASP B 595 " pdb=" CG ASP B 595 " pdb=" OD1 ASP B 595 " ideal model delta sinusoidal sigma weight residual -30.00 -74.43 44.43 1 2.00e+01 2.50e-03 6.86e+00 dihedral pdb=" N ASP B 650 " pdb=" C ASP B 650 " pdb=" CA ASP B 650 " pdb=" CB ASP B 650 " ideal model delta harmonic sigma weight residual 122.80 116.39 6.41 0 2.50e+00 1.60e-01 6.57e+00 ... (remaining 1768 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.097: 371 0.097 - 0.193: 99 0.193 - 0.290: 16 0.290 - 0.387: 3 0.387 - 0.483: 2 Chirality restraints: 491 Sorted by residual: chirality pdb=" CG LEU B 264 " pdb=" CB LEU B 264 " pdb=" CD1 LEU B 264 " pdb=" CD2 LEU B 264 " both_signs ideal model delta sigma weight residual False -2.59 -3.07 0.48 2.00e-01 2.50e+01 5.84e+00 chirality pdb=" CB ILE B 285 " pdb=" CA ILE B 285 " pdb=" CG1 ILE B 285 " pdb=" CG2 ILE B 285 " both_signs ideal model delta sigma weight residual False 2.64 3.05 -0.40 2.00e-01 2.50e+01 4.06e+00 chirality pdb=" CA TRP B 304 " pdb=" N TRP B 304 " pdb=" C TRP B 304 " pdb=" CB TRP B 304 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.19e+00 ... (remaining 488 not shown) Planarity restraints: 493 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL B 697 " 0.015 2.00e-02 2.50e+03 3.07e-02 9.41e+00 pdb=" C VAL B 697 " -0.053 2.00e-02 2.50e+03 pdb=" O VAL B 697 " 0.020 2.00e-02 2.50e+03 pdb=" N ASN B 698 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 675 " 0.035 2.00e-02 2.50e+03 1.98e-02 7.85e+00 pdb=" CG TYR B 675 " -0.010 2.00e-02 2.50e+03 pdb=" CD1 TYR B 675 " -0.016 2.00e-02 2.50e+03 pdb=" CD2 TYR B 675 " -0.012 2.00e-02 2.50e+03 pdb=" CE1 TYR B 675 " -0.011 2.00e-02 2.50e+03 pdb=" CE2 TYR B 675 " -0.013 2.00e-02 2.50e+03 pdb=" CZ TYR B 675 " -0.005 2.00e-02 2.50e+03 pdb=" OH TYR B 675 " 0.033 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN B 741 " -0.012 2.00e-02 2.50e+03 2.42e-02 5.86e+00 pdb=" C ASN B 741 " 0.042 2.00e-02 2.50e+03 pdb=" O ASN B 741 " -0.016 2.00e-02 2.50e+03 pdb=" N LEU B 742 " -0.014 2.00e-02 2.50e+03 ... (remaining 490 not shown) Histogram of nonbonded interaction distances: 2.39 - 2.89: 1125 2.89 - 3.39: 2994 3.39 - 3.89: 4759 3.89 - 4.40: 5429 4.40 - 4.90: 8451 Nonbonded interactions: 22758 Sorted by model distance: nonbonded pdb=" OD1 ASP B 737 " pdb=" NZ LYS B 739 " model vdw 2.386 3.120 nonbonded pdb=" N VAL B 697 " pdb=" N ASN B 698 " model vdw 2.467 2.560 nonbonded pdb=" N ASN B 711 " pdb=" O ASN B 711 " model vdw 2.498 2.496 nonbonded pdb=" N PRO B 646 " pdb=" O PRO B 646 " model vdw 2.533 2.496 nonbonded pdb=" N ASN B 613 " pdb=" O ASN B 613 " model vdw 2.553 2.496 ... (remaining 22753 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: 0.970 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 13.800 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: 0.010 Load rotamer database and sin/cos tables:12.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7577 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 : 0.022 0.132 2980 Z= 1.484 Angle : 1.511 8.243 4039 Z= 1.034 Chirality : 0.093 0.483 491 Planarity : 0.008 0.031 493 Dihedral : 10.569 71.622 1051 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 0.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.83 % Favored : 99.17 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: 1.84 (0.41), residues: 361 helix: 1.41 (0.30), residues: 223 sheet: 0.94 (0.88), residues: 42 loop : 1.21 (0.65), residues: 96 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.008 TRP B 683 HIS 0.005 0.002 HIS B 346 PHE 0.019 0.005 PHE B 682 TYR 0.035 0.008 TYR B 675 ARG 0.005 0.001 ARG B 338 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 722 Ramachandran restraints generated. 361 Oldfield, 0 Emsley, 361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 722 Ramachandran restraints generated. 361 Oldfield, 0 Emsley, 361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 99 time to evaluate : 0.329 Fit side-chains revert: symmetry clash REVERT: B 526 LYS cc_start: 0.7984 (mttt) cc_final: 0.7595 (mtpp) REVERT: B 624 LYS cc_start: 0.8434 (mmtm) cc_final: 0.7572 (tttp) REVERT: B 702 MET cc_start: 0.8860 (mtt) cc_final: 0.8638 (mtp) outliers start: 0 outliers final: 1 residues processed: 99 average time/residue: 1.1515 time to fit residues: 116.8400 Evaluate side-chains 85 residues out of total 344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 84 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 560 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 31 optimal weight: 0.0050 chunk 28 optimal weight: 2.9990 chunk 15 optimal weight: 0.8980 chunk 9 optimal weight: 0.7980 chunk 18 optimal weight: 0.9980 chunk 14 optimal weight: 0.7980 chunk 29 optimal weight: 0.8980 chunk 11 optimal weight: 6.9990 chunk 17 optimal weight: 0.8980 chunk 21 optimal weight: 0.6980 chunk 33 optimal weight: 0.7980 overall best weight: 0.6194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 531 GLN B 605 ASN B 648 GLN B 688 ASN B 698 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7533 moved from start: 0.2469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 2980 Z= 0.189 Angle : 0.488 6.378 4039 Z= 0.262 Chirality : 0.041 0.144 491 Planarity : 0.003 0.040 493 Dihedral : 8.461 54.637 397 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 2.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.83 % Favored : 99.17 % Rotamer: Outliers : 4.56 % Allowed : 9.12 % Favored : 86.32 % 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: 2.74 (0.43), residues: 361 helix: 2.50 (0.32), residues: 229 sheet: 0.48 (0.76), residues: 42 loop : 0.76 (0.68), residues: 90 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 281 HIS 0.002 0.001 HIS B 592 PHE 0.012 0.002 PHE B 271 TYR 0.005 0.001 TYR B 740 ARG 0.004 0.001 ARG B 720 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 722 Ramachandran restraints generated. 361 Oldfield, 0 Emsley, 361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 722 Ramachandran restraints generated. 361 Oldfield, 0 Emsley, 361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 90 time to evaluate : 0.336 Fit side-chains revert: symmetry clash REVERT: B 301 PHE cc_start: 0.7152 (t80) cc_final: 0.6945 (t80) outliers start: 14 outliers final: 6 residues processed: 95 average time/residue: 1.2267 time to fit residues: 119.3836 Evaluate side-chains 91 residues out of total 344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 85 time to evaluate : 0.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 264 LEU Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 541 ILE Chi-restraints excluded: chain B residue 543 MET Chi-restraints excluded: chain B residue 560 ILE Chi-restraints excluded: chain B residue 562 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 18 optimal weight: 0.9990 chunk 10 optimal weight: 2.9990 chunk 27 optimal weight: 0.8980 chunk 22 optimal weight: 0.1980 chunk 9 optimal weight: 0.8980 chunk 33 optimal weight: 0.5980 chunk 36 optimal weight: 0.6980 chunk 29 optimal weight: 0.9980 chunk 11 optimal weight: 6.9990 chunk 25 optimal weight: 0.6980 chunk 17 optimal weight: 0.7980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 531 GLN B 688 ASN B 698 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7540 moved from start: 0.2988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 2980 Z= 0.186 Angle : 0.453 6.916 4039 Z= 0.240 Chirality : 0.039 0.138 491 Planarity : 0.003 0.030 493 Dihedral : 7.947 53.751 397 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 2.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.83 % Favored : 99.17 % Rotamer: Outliers : 3.26 % Allowed : 12.05 % Favored : 84.69 % 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: 3.13 (0.43), residues: 361 helix: 2.91 (0.32), residues: 229 sheet: 0.56 (0.76), residues: 42 loop : 0.64 (0.68), residues: 90 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 316 HIS 0.003 0.001 HIS B 708 PHE 0.011 0.002 PHE B 654 TYR 0.008 0.001 TYR B 740 ARG 0.003 0.000 ARG B 720 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 722 Ramachandran restraints generated. 361 Oldfield, 0 Emsley, 361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 722 Ramachandran restraints generated. 361 Oldfield, 0 Emsley, 361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 88 time to evaluate : 0.304 Fit side-chains revert: symmetry clash REVERT: B 624 LYS cc_start: 0.8452 (mmtm) cc_final: 0.7842 (tmmt) outliers start: 10 outliers final: 6 residues processed: 92 average time/residue: 1.1744 time to fit residues: 110.7269 Evaluate side-chains 91 residues out of total 344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 85 time to evaluate : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 300 GLU Chi-restraints excluded: chain B residue 317 LEU Chi-restraints excluded: chain B residue 543 MET Chi-restraints excluded: chain B residue 560 ILE Chi-restraints excluded: chain B residue 562 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 3 optimal weight: 5.9990 chunk 16 optimal weight: 0.6980 chunk 22 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 35 optimal weight: 0.6980 chunk 17 optimal weight: 0.8980 chunk 32 optimal weight: 0.9990 chunk 9 optimal weight: 0.6980 chunk 29 optimal weight: 0.6980 chunk 20 optimal weight: 0.5980 chunk 0 optimal weight: 10.0000 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 525 ASN B 531 GLN B 688 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7547 moved from start: 0.3195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 2980 Z= 0.196 Angle : 0.448 7.284 4039 Z= 0.233 Chirality : 0.039 0.137 491 Planarity : 0.002 0.030 493 Dihedral : 7.815 56.110 397 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 3.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 3.58 % Allowed : 14.33 % Favored : 82.08 % 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: 3.25 (0.44), residues: 361 helix: 3.07 (0.32), residues: 229 sheet: 0.70 (0.79), residues: 42 loop : 0.42 (0.67), residues: 90 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 548 HIS 0.004 0.001 HIS B 708 PHE 0.011 0.001 PHE B 271 TYR 0.007 0.001 TYR B 740 ARG 0.002 0.000 ARG B 720 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 722 Ramachandran restraints generated. 361 Oldfield, 0 Emsley, 361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 722 Ramachandran restraints generated. 361 Oldfield, 0 Emsley, 361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 87 time to evaluate : 0.296 Fit side-chains revert: symmetry clash REVERT: B 316 TRP cc_start: 0.8298 (t-100) cc_final: 0.8047 (t-100) REVERT: B 624 LYS cc_start: 0.8473 (mmtm) cc_final: 0.7934 (tmmt) outliers start: 11 outliers final: 8 residues processed: 90 average time/residue: 1.1374 time to fit residues: 104.9574 Evaluate side-chains 93 residues out of total 344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 85 time to evaluate : 0.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 300 GLU Chi-restraints excluded: chain B residue 525 ASN Chi-restraints excluded: chain B residue 560 ILE Chi-restraints excluded: chain B residue 562 LEU Chi-restraints excluded: chain B residue 563 LEU Chi-restraints excluded: chain B residue 579 LYS Chi-restraints excluded: chain B residue 662 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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-5409/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 766, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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-5409/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-5409/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-5409/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-5409/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-5409/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-5409/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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-5409/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-5409/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-dev-5409/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-dev-5409/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: 54.6432 > 50: distance: 20 - 39: 10.134 distance: 24 - 46: 29.530 distance: 29 - 54: 18.839 distance: 32 - 39: 8.610 distance: 33 - 65: 4.492 distance: 39 - 40: 3.511 distance: 40 - 41: 14.060 distance: 40 - 43: 4.892 distance: 41 - 42: 18.981 distance: 41 - 46: 29.560 distance: 42 - 74: 20.924 distance: 43 - 44: 10.070 distance: 43 - 45: 3.613 distance: 46 - 47: 35.695 distance: 47 - 48: 10.052 distance: 47 - 50: 16.552 distance: 48 - 49: 12.900 distance: 48 - 54: 12.275 distance: 49 - 79: 14.598 distance: 50 - 51: 33.151 distance: 50 - 52: 21.597 distance: 51 - 53: 9.348 distance: 54 - 55: 13.627 distance: 55 - 56: 8.557 distance: 55 - 58: 8.218 distance: 56 - 57: 5.117 distance: 56 - 65: 7.755 distance: 57 - 87: 7.650 distance: 58 - 59: 13.612 distance: 59 - 60: 10.223 distance: 59 - 61: 10.990 distance: 60 - 62: 7.286 distance: 61 - 63: 8.181 distance: 62 - 64: 7.501 distance: 63 - 64: 11.602 distance: 65 - 66: 5.731 distance: 66 - 67: 4.002 distance: 66 - 69: 6.104 distance: 68 - 95: 11.683 distance: 69 - 70: 4.947 distance: 70 - 71: 6.595 distance: 71 - 72: 13.407 distance: 71 - 73: 8.569 distance: 75 - 76: 3.242 distance: 75 - 78: 6.635 distance: 76 - 77: 9.171 distance: 76 - 79: 9.580 distance: 77 - 106: 21.732 distance: 79 - 80: 3.362 distance: 80 - 81: 4.128 distance: 80 - 83: 7.455 distance: 81 - 82: 4.634 distance: 81 - 87: 5.078 distance: 82 - 113: 14.427 distance: 83 - 84: 13.649 distance: 83 - 85: 12.868 distance: 84 - 86: 9.114 distance: 88 - 89: 4.949 distance: 88 - 91: 5.971 distance: 89 - 90: 3.263 distance: 89 - 95: 4.227 distance: 90 - 124: 9.526 distance: 91 - 92: 5.566 distance: 91 - 93: 14.832 distance: 92 - 94: 13.750 distance: 97 - 98: 8.338 distance: 97 - 106: 7.741 distance: 99 - 100: 6.716 distance: 100 - 101: 13.941 distance: 100 - 102: 6.143 distance: 101 - 103: 3.510 distance: 102 - 104: 9.724 distance: 103 - 105: 4.670 distance: 104 - 105: 8.517 distance: 106 - 107: 3.520 distance: 107 - 108: 3.504 distance: 107 - 110: 5.458 distance: 110 - 111: 5.972 distance: 110 - 112: 9.984 distance: 113 - 114: 8.667 distance: 114 - 115: 5.428 distance: 114 - 117: 15.030 distance: 115 - 116: 12.926 distance: 115 - 124: 3.603 distance: 117 - 118: 4.405 distance: 118 - 119: 12.740 distance: 118 - 120: 6.633 distance: 119 - 121: 10.170 distance: 120 - 122: 8.058 distance: 121 - 123: 6.537 distance: 122 - 123: 13.705