Starting phenix.real_space_refine on Sun Apr 27 02:44:16 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7lkf_23405/04_2025/7lkf_23405.cif Found real_map, /net/cci-nas-00/data/ceres_data/7lkf_23405/04_2025/7lkf_23405.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7lkf_23405/04_2025/7lkf_23405.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7lkf_23405/04_2025/7lkf_23405.map" model { file = "/net/cci-nas-00/data/ceres_data/7lkf_23405/04_2025/7lkf_23405.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7lkf_23405/04_2025/7lkf_23405.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.005 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 8 5.16 5 C 2634 2.51 5 N 710 2.21 5 O 787 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 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: 4139 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2298 Number of conformers: 1 Conformer: "" Number of residues, atoms: 281, 2298 Classifications: {'peptide': 281} Link IDs: {'PTRANS': 22, 'TRANS': 258} Chain breaks: 3 Chain: "H" Number of atoms: 959 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 959 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 4, 'TRANS': 116} Chain: "L" Number of atoms: 854 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 854 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 3, 'TRANS': 105} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 3.83, per 1000 atoms: 0.93 Number of scatterers: 4139 At special positions: 0 Unit cell: (74.52, 91.8, 95.04, 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 8 16.00 O 787 8.00 N 710 7.00 C 2634 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 147 " - pdb=" SG CYS A 169 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 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 BETA1-4 " NAG B 1 " - " NAG B 2 " NAG-ASN " NAG B 1 " - " ASN A 667 " Time building additional restraints: 1.02 Conformation dependent library (CDL) restraints added in 460.3 milliseconds 998 Ramachandran restraints generated. 499 Oldfield, 0 Emsley, 499 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 964 Finding SS restraints... Secondary structure from input PDB file: 19 helices and 8 sheets defined 25.8% alpha, 31.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.53 Creating SS restraints... Processing helix chain 'A' and resid 110 through 114 Processing helix chain 'A' and resid 115 through 121 removed outlier: 3.716A pdb=" N ARG A 121 " --> pdb=" O SER A 117 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 132 Processing helix chain 'A' and resid 142 through 146 Processing helix chain 'A' and resid 157 through 161 removed outlier: 3.899A pdb=" N LEU A 160 " --> pdb=" O LEU A 157 " (cutoff:3.500A) Processing helix chain 'A' and resid 173 through 179 Processing helix chain 'A' and resid 181 through 187 Processing helix chain 'A' and resid 190 through 197 Processing helix chain 'A' and resid 208 through 215 Processing helix chain 'A' and resid 244 through 259 Processing helix chain 'A' and resid 644 through 648 Processing helix chain 'A' and resid 649 through 654 Processing helix chain 'A' and resid 657 through 665 removed outlier: 3.601A pdb=" N TYR A 665 " --> pdb=" O SER A 661 " (cutoff:3.500A) Processing helix chain 'A' and resid 688 through 695 Processing helix chain 'A' and resid 697 through 701 removed outlier: 3.513A pdb=" N ALA A 701 " --> pdb=" O PRO A 698 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 32 Processing helix chain 'H' and resid 62 through 65 removed outlier: 3.777A pdb=" N GLN H 65 " --> pdb=" O PRO H 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 62 through 65' Processing helix chain 'H' and resid 87 through 91 Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.831A pdb=" N ILE L 83 " --> pdb=" O GLN L 80 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 61 through 64 removed outlier: 6.301A pdb=" N VAL A 61 " --> pdb=" O ILE A 271 " (cutoff:3.500A) removed outlier: 7.485A pdb=" N HIS A 273 " --> pdb=" O VAL A 61 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N ASP A 63 " --> pdb=" O HIS A 273 " (cutoff:3.500A) removed outlier: 7.961A pdb=" N HIS A 275 " --> pdb=" O ASP A 63 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 61 through 64 removed outlier: 6.301A pdb=" N VAL A 61 " --> pdb=" O ILE A 271 " (cutoff:3.500A) removed outlier: 7.485A pdb=" N HIS A 273 " --> pdb=" O VAL A 61 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N ASP A 63 " --> pdb=" O HIS A 273 " (cutoff:3.500A) removed outlier: 7.961A pdb=" N HIS A 275 " --> pdb=" O ASP A 63 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 149 through 150 Processing sheet with id=AA4, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AA5, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.473A pdb=" N ILE H 34 " --> pdb=" O ARG H 50 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N ARG H 50 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'L' and resid 4 through 6 Processing sheet with id=AA7, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.562A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'L' and resid 10 through 13 removed outlier: 3.748A pdb=" N THR L 97 " --> pdb=" O GLN L 90 " (cutoff:3.500A) 164 hydrogen bonds defined for protein. 384 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: 1.14 Time building geometry restraints manager: 1.21 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1333 1.34 - 1.46: 774 1.46 - 1.57: 2127 1.57 - 1.69: 0 1.69 - 1.81: 9 Bond restraints: 4243 Sorted by residual: bond pdb=" N GLY A 636 " pdb=" CA GLY A 636 " ideal model delta sigma weight residual 1.451 1.492 -0.041 1.60e-02 3.91e+03 6.49e+00 bond pdb=" N GLY A 53 " pdb=" CA GLY A 53 " ideal model delta sigma weight residual 1.451 1.491 -0.040 1.60e-02 3.91e+03 6.13e+00 bond pdb=" C1 NAG B 2 " pdb=" O5 NAG B 2 " ideal model delta sigma weight residual 1.406 1.440 -0.034 2.00e-02 2.50e+03 2.92e+00 bond pdb=" N ASP L 1 " pdb=" CA ASP L 1 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.87e+00 bond pdb=" N GLU H 1 " pdb=" CA GLU H 1 " ideal model delta sigma weight residual 1.458 1.489 -0.031 1.90e-02 2.77e+03 2.70e+00 ... (remaining 4238 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.39: 5513 1.39 - 2.77: 200 2.77 - 4.16: 45 4.16 - 5.55: 10 5.55 - 6.94: 1 Bond angle restraints: 5769 Sorted by residual: angle pdb=" CA PRO A 155 " pdb=" N PRO A 155 " pdb=" CD PRO A 155 " ideal model delta sigma weight residual 112.00 107.82 4.18 1.40e+00 5.10e-01 8.91e+00 angle pdb=" CA TYR H 99 " pdb=" CB TYR H 99 " pdb=" CG TYR H 99 " ideal model delta sigma weight residual 113.90 118.96 -5.06 1.80e+00 3.09e-01 7.91e+00 angle pdb=" N ASP H 103 " pdb=" CA ASP H 103 " pdb=" C ASP H 103 " ideal model delta sigma weight residual 113.18 109.67 3.51 1.33e+00 5.65e-01 6.95e+00 angle pdb=" N ASP A 190 " pdb=" CA ASP A 190 " pdb=" C ASP A 190 " ideal model delta sigma weight residual 107.37 112.16 -4.79 2.07e+00 2.33e-01 5.35e+00 angle pdb=" N THR L 51 " pdb=" CA THR L 51 " pdb=" C THR L 51 " ideal model delta sigma weight residual 110.80 115.21 -4.41 2.13e+00 2.20e-01 4.30e+00 ... (remaining 5764 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.68: 2362 17.68 - 35.36: 158 35.36 - 53.04: 20 53.04 - 70.72: 9 70.72 - 88.40: 7 Dihedral angle restraints: 2556 sinusoidal: 1060 harmonic: 1496 Sorted by residual: dihedral pdb=" CB CYS A 147 " pdb=" SG CYS A 147 " pdb=" SG CYS A 169 " pdb=" CB CYS A 169 " ideal model delta sinusoidal sigma weight residual -86.00 -162.43 76.43 1 1.00e+01 1.00e-02 7.35e+01 dihedral pdb=" CA THR L 93 " pdb=" C THR L 93 " pdb=" N LEU L 94 " pdb=" CA LEU L 94 " ideal model delta harmonic sigma weight residual -180.00 -151.68 -28.32 0 5.00e+00 4.00e-02 3.21e+01 dihedral pdb=" CA PRO A 155 " pdb=" C PRO A 155 " pdb=" N GLY A 156 " pdb=" CA GLY A 156 " ideal model delta harmonic sigma weight residual 180.00 154.56 25.44 0 5.00e+00 4.00e-02 2.59e+01 ... (remaining 2553 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 550 0.062 - 0.124: 80 0.124 - 0.186: 8 0.186 - 0.248: 0 0.248 - 0.310: 1 Chirality restraints: 639 Sorted by residual: chirality pdb=" C1 NAG B 1 " pdb=" ND2 ASN A 667 " pdb=" C2 NAG B 1 " pdb=" O5 NAG B 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.09 -0.31 2.00e-01 2.50e+01 2.41e+00 chirality pdb=" CA LEU L 94 " pdb=" N LEU L 94 " pdb=" C LEU L 94 " pdb=" CB LEU L 94 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.42e-01 chirality pdb=" CA ILE A 271 " pdb=" N ILE A 271 " pdb=" C ILE A 271 " pdb=" CB ILE A 271 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.92e-01 ... (remaining 636 not shown) Planarity restraints: 737 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 154 " -0.070 5.00e-02 4.00e+02 1.05e-01 1.77e+01 pdb=" N PRO A 155 " 0.182 5.00e-02 4.00e+02 pdb=" CA PRO A 155 " -0.054 5.00e-02 4.00e+02 pdb=" CD PRO A 155 " -0.057 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER A 117 " 0.026 5.00e-02 4.00e+02 3.98e-02 2.53e+00 pdb=" N PRO A 118 " -0.069 5.00e-02 4.00e+02 pdb=" CA PRO A 118 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 118 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR H 99 " -0.002 2.00e-02 2.50e+03 1.08e-02 2.33e+00 pdb=" CG TYR H 99 " -0.015 2.00e-02 2.50e+03 pdb=" CD1 TYR H 99 " 0.005 2.00e-02 2.50e+03 pdb=" CD2 TYR H 99 " 0.022 2.00e-02 2.50e+03 pdb=" CE1 TYR H 99 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR H 99 " -0.014 2.00e-02 2.50e+03 pdb=" CZ TYR H 99 " 0.003 2.00e-02 2.50e+03 pdb=" OH TYR H 99 " -0.001 2.00e-02 2.50e+03 ... (remaining 734 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 56 2.66 - 3.22: 3758 3.22 - 3.78: 5969 3.78 - 4.34: 8951 4.34 - 4.90: 14737 Nonbonded interactions: 33471 Sorted by model distance: nonbonded pdb=" O3 NAG B 1 " pdb=" O7 NAG B 2 " model vdw 2.101 3.040 nonbonded pdb=" O GLY A 87 " pdb=" OH TYR A 674 " model vdw 2.199 3.040 nonbonded pdb=" O ARG A 161 " pdb=" OD1 ASN A 162 " model vdw 2.350 3.040 nonbonded pdb=" OD1 ASP L 17 " pdb=" N ARG L 18 " model vdw 2.358 3.120 nonbonded pdb=" O ASN L 31 " pdb=" OG1 THR L 51 " model vdw 2.393 3.040 ... (remaining 33466 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.490 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 15.110 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 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:13.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 4248 Z= 0.213 Angle : 0.675 6.936 5781 Z= 0.376 Chirality : 0.047 0.310 639 Planarity : 0.005 0.105 736 Dihedral : 12.764 88.404 1583 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % 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: -0.59 (0.37), residues: 499 helix: 0.37 (0.64), residues: 73 sheet: -0.29 (0.39), residues: 173 loop : -0.59 (0.38), residues: 253 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 110 HIS 0.004 0.001 HIS A 273 PHE 0.021 0.002 PHE A 97 TYR 0.022 0.002 TYR H 99 ARG 0.012 0.001 ARG A 230 Details of bonding type rmsd link_NAG-ASN : bond 0.00642 ( 1) link_NAG-ASN : angle 1.31730 ( 3) link_BETA1-4 : bond 0.00955 ( 1) link_BETA1-4 : angle 4.07060 ( 3) hydrogen bonds : bond 0.07942 ( 154) hydrogen bonds : angle 5.57887 ( 384) SS BOND : bond 0.00765 ( 3) SS BOND : angle 1.53022 ( 6) covalent geometry : bond 0.00461 ( 4243) covalent geometry : angle 0.66646 ( 5769) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 998 Ramachandran restraints generated. 499 Oldfield, 0 Emsley, 499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 998 Ramachandran restraints generated. 499 Oldfield, 0 Emsley, 499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 83 time to evaluate : 0.452 Fit side-chains REVERT: A 128 GLU cc_start: 0.7583 (tp30) cc_final: 0.7380 (tp30) outliers start: 0 outliers final: 0 residues processed: 83 average time/residue: 1.5641 time to fit residues: 133.3954 Evaluate side-chains 56 residues out of total 455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 56 time to evaluate : 0.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 42 optimal weight: 0.4980 chunk 37 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 chunk 12 optimal weight: 0.6980 chunk 25 optimal weight: 0.9980 chunk 20 optimal weight: 1.9990 chunk 39 optimal weight: 2.9990 chunk 15 optimal weight: 0.9980 chunk 23 optimal weight: 0.7980 chunk 29 optimal weight: 0.3980 chunk 45 optimal weight: 1.9990 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 95 GLN A 697 HIS H 57 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.127514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.099115 restraints weight = 5124.270| |-----------------------------------------------------------------------------| r_work (start): 0.2983 rms_B_bonded: 2.42 r_work: 0.2816 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.2816 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 moved from start: 0.1080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4248 Z= 0.143 Angle : 0.611 6.847 5781 Z= 0.308 Chirality : 0.046 0.165 639 Planarity : 0.004 0.052 736 Dihedral : 5.146 25.106 605 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 2.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 1.32 % Allowed : 10.55 % Favored : 88.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.29 (0.38), residues: 499 helix: 0.43 (0.65), residues: 73 sheet: -0.18 (0.39), residues: 172 loop : -0.25 (0.40), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP L 96 HIS 0.003 0.001 HIS A 273 PHE 0.020 0.001 PHE A 97 TYR 0.036 0.002 TYR H 99 ARG 0.004 0.001 ARG H 59 Details of bonding type rmsd link_NAG-ASN : bond 0.00068 ( 1) link_NAG-ASN : angle 0.80989 ( 3) link_BETA1-4 : bond 0.00923 ( 1) link_BETA1-4 : angle 2.36782 ( 3) hydrogen bonds : bond 0.03188 ( 154) hydrogen bonds : angle 5.07634 ( 384) SS BOND : bond 0.00546 ( 3) SS BOND : angle 1.27396 ( 6) covalent geometry : bond 0.00343 ( 4243) covalent geometry : angle 0.60733 ( 5769) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 998 Ramachandran restraints generated. 499 Oldfield, 0 Emsley, 499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 998 Ramachandran restraints generated. 499 Oldfield, 0 Emsley, 499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 61 time to evaluate : 0.496 Fit side-chains REVERT: A 128 GLU cc_start: 0.7719 (tp30) cc_final: 0.7350 (tp30) outliers start: 6 outliers final: 2 residues processed: 65 average time/residue: 1.7758 time to fit residues: 118.6133 Evaluate side-chains 56 residues out of total 455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 54 time to evaluate : 0.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 ASP Chi-restraints excluded: chain H residue 21 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 21 optimal weight: 2.9990 chunk 5 optimal weight: 0.9980 chunk 1 optimal weight: 1.9990 chunk 16 optimal weight: 0.6980 chunk 14 optimal weight: 0.9980 chunk 49 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 39 optimal weight: 4.9990 chunk 3 optimal weight: 0.8980 chunk 19 optimal weight: 0.0870 chunk 7 optimal weight: 0.0970 overall best weight: 0.5556 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 65 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.126244 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.096542 restraints weight = 5176.975| |-----------------------------------------------------------------------------| r_work (start): 0.3085 rms_B_bonded: 2.48 r_work: 0.2925 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.2925 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 moved from start: 0.1411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 4248 Z= 0.121 Angle : 0.560 5.909 5781 Z= 0.282 Chirality : 0.044 0.163 639 Planarity : 0.004 0.038 736 Dihedral : 4.755 22.625 605 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 2.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 1.54 % Allowed : 14.07 % Favored : 84.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.09 (0.39), residues: 499 helix: 0.55 (0.66), residues: 73 sheet: -0.05 (0.39), residues: 166 loop : -0.12 (0.41), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 47 HIS 0.003 0.001 HIS A 697 PHE 0.019 0.001 PHE A 97 TYR 0.026 0.001 TYR H 99 ARG 0.004 0.000 ARG L 18 Details of bonding type rmsd link_NAG-ASN : bond 0.00054 ( 1) link_NAG-ASN : angle 1.07250 ( 3) link_BETA1-4 : bond 0.00824 ( 1) link_BETA1-4 : angle 2.20813 ( 3) hydrogen bonds : bond 0.02952 ( 154) hydrogen bonds : angle 4.85064 ( 384) SS BOND : bond 0.00576 ( 3) SS BOND : angle 1.18403 ( 6) covalent geometry : bond 0.00287 ( 4243) covalent geometry : angle 0.55630 ( 5769) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 998 Ramachandran restraints generated. 499 Oldfield, 0 Emsley, 499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 998 Ramachandran restraints generated. 499 Oldfield, 0 Emsley, 499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 56 time to evaluate : 0.476 Fit side-chains REVERT: A 145 GLU cc_start: 0.8332 (mt-10) cc_final: 0.8083 (mt-10) REVERT: L 45 LYS cc_start: 0.8915 (tttt) cc_final: 0.8698 (tttt) outliers start: 7 outliers final: 3 residues processed: 61 average time/residue: 1.8438 time to fit residues: 116.3839 Evaluate side-chains 56 residues out of total 455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 53 time to evaluate : 0.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 ASP Chi-restraints excluded: chain A residue 673 ARG Chi-restraints excluded: chain H residue 21 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- 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: 73.6425 > 50: distance: 9 - 34: 31.539 distance: 16 - 43: 31.998 distance: 20 - 51: 36.628 distance: 29 - 34: 34.963 distance: 30 - 59: 37.574 distance: 34 - 35: 41.259 distance: 35 - 36: 28.505 distance: 35 - 38: 28.845 distance: 36 - 43: 38.412 distance: 38 - 39: 70.036 distance: 39 - 40: 57.652 distance: 40 - 41: 39.400 distance: 41 - 42: 55.962 distance: 43 - 44: 40.223 distance: 45 - 46: 55.736 distance: 45 - 51: 40.576 distance: 47 - 48: 44.476 distance: 48 - 49: 46.334 distance: 48 - 50: 42.941 distance: 52 - 53: 65.161 distance: 52 - 55: 57.876 distance: 53 - 54: 65.689 distance: 53 - 59: 56.127 distance: 55 - 56: 55.831 distance: 56 - 57: 56.913 distance: 56 - 58: 57.147 distance: 59 - 60: 40.894 distance: 60 - 61: 39.405 distance: 60 - 63: 40.530 distance: 61 - 62: 40.971 distance: 61 - 69: 56.496 distance: 63 - 64: 56.295 distance: 64 - 65: 56.126 distance: 64 - 66: 41.165 distance: 66 - 68: 50.968 distance: 67 - 68: 39.414 distance: 69 - 70: 39.876 distance: 69 - 75: 56.859 distance: 70 - 71: 38.731 distance: 70 - 73: 39.585 distance: 71 - 76: 41.288 distance: 73 - 74: 56.631 distance: 76 - 77: 56.421 distance: 77 - 80: 70.107 distance: 78 - 79: 40.001 distance: 78 - 82: 55.418 distance: 80 - 81: 40.768 distance: 82 - 83: 44.702 distance: 82 - 88: 40.101 distance: 83 - 84: 42.540 distance: 83 - 86: 17.272 distance: 84 - 85: 58.149 distance: 84 - 89: 57.063 distance: 86 - 87: 57.188 distance: 87 - 88: 55.808 distance: 90 - 91: 39.268 distance: 90 - 93: 40.267 distance: 91 - 92: 56.291 distance: 91 - 97: 56.449 distance: 93 - 94: 56.895 distance: 94 - 95: 41.056 distance: 94 - 96: 44.186 distance: 97 - 98: 39.717 distance: 98 - 99: 60.355 distance: 98 - 101: 39.185 distance: 99 - 100: 43.782 distance: 99 - 103: 19.779 distance: 101 - 102: 69.152 distance: 103 - 104: 51.498 distance: 104 - 105: 55.944 distance: 104 - 107: 40.260 distance: 105 - 106: 40.006 distance: 105 - 110: 33.203 distance: 107 - 109: 38.738