Tue 25 Dec 19:27:57 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir Job ID is set to 2fur-3.8-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2fur-3.8-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2fur-3.8-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2fur-3.8-parrot-hancs Accepted label: fp=FP Accepted label: sigfp=SIGFP Accepted label: phibest=hltofom.Phi_fom.phi Accepted label: fom=hltofom.Phi_fom.fom mtz labels taken: FP SIGFP hltofom.Phi_fom.phi hltofom.Phi_fom.fom Parameter file /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2fur-3.8-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2fur-3.8-parrot-hancs ############### You are running ARP/wARP 8.0 ############### ============================================================ Please cite at least one of the publications below for the ARP/wARP application you are using: Lamzin VS, Wilson KS. (1993) Automated refinement of protein models. Acta Crystallogr D Biol Crystallogr. 49, 129-147 Morris RJ, Perrakis A. Lamzin VS. (2003) ARP/wARP and automatic interpretation of protein electron density maps. In Methods Enzymol. (Carter, C.W. & Sweet, R.M. eds.) 374, 229-244 Langer GG, Hazledine S, Wiegels T, Carolan C, Lamzin VS. (2013) Visual automated macromolecular model building. Acta Crystallogr D Biol Crystallogr. 69, 635-641 Use of Refmac is an essential part of model building with ARP/wARP. Please acknowledge the use of Refmac by citing the following publication: Murshudov GN, Skubak P, Lebedev AA, Pannu NS, Steiner RA, Nicholls RA, Winn MD, Long F, Vagin AA. (2011) REFMAC5 for the refinement of macromolecular crystal structures. Acta Crystallogr D Biol Crystallogr. 67, 355-367 ============================================================ Tue 25 Dec 19:28:07 GMT 2018 You are running ARP/wARP version 8.0 Entering warp_tracing.sh from COMMAND_LINE_SUBMISSION The working directory: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2fur-3.8-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2fur-3.8-parrot-hancs/arp_warp_classic.par ARP/wARP will run in subdirectory: temp_tracing Checking the estimated solvent content Computed solvent content is outside allowed range. Target number of residues/nucleotides is changed to 250 and 0 Target number of residues in the AU: 250 Target solvent content: 0.6674 Checking the provided sequence file Detected sequence length: 209 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 418 Adjusted target solvent content: 0.44 Input MTZ file: 2fur-3.8-parrot-hancs.mtz.cad Column labels for model refinement: FP SIGFP Column labels to obtain initial map: FP hltofom.Phi_fom.phi hltofom.Phi_fom.fom Space group number: 19 Cell parameters: 61.040 66.690 99.940 90.000 90.000 90.000 Input sequence file: 2fur-3.8-parrot-hancs.fasta_lf Building free atoms model in initial map for 3344 target number of atoms Had to go as low as 0.70 sigma, to complete atoms search. ARP/wARP will be iterated with REFMAC5 50 refinement / model update cycles will be run in total. Atoms will be removed below 1.0 sigma in 2mFoDFc map and added above 3.2 sigma in mFoDFc map. Refmac Refinement Parameters 3 REFMAC cycle(s) with 1.0 1.0 fractional shifts damping in each cycle. Conditional restraints will be used Weight for restraints is set to AUTO Solvent mask correction will be used Anisotropic scaling with no bulk solvent correction Model Building Parameters Main chain tracing will take place every 5 refinement / model update cycles. Side chain docking will be performed from autobuilding cycle number 1 NCS extension will be performed at every building cycle. NCS restraints will be applied at each refinement cycle. Loops will be built when appropriate and at the last cycle Resolution range: 55.473 3.800 Wilson plot Bfac: 89.68 4300 reflections ( 99.54 % complete ) and 0 restraints for refining 3706 atoms. Observations/parameters ratio is 0.29 ------------------------------------------------------ Starting model: R = 0.3255 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2981 (Rfree = 0.000) for 3706 atoms. Found 11 (20 requested) and removed 40 (10 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.76 4.07 Search for helices and strands: 0 residues in 0 chains, 3756 seeds are put forward NCS extension: 0 residues added, 3756 seeds are put forward Round 1: 159 peptides, 31 chains. Longest chain 9 peptides. Score 0.325 Round 2: 203 peptides, 29 chains. Longest chain 19 peptides. Score 0.525 Round 3: 222 peptides, 31 chains. Longest chain 28 peptides. Score 0.558 Round 4: 224 peptides, 28 chains. Longest chain 17 peptides. Score 0.605 Round 5: 224 peptides, 30 chains. Longest chain 21 peptides. Score 0.578 Taking the results from Round 4 Chains 28, Residues 196, Estimated correctness of the model 1.2 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4300 reflections ( 99.54 % complete ) and 6956 restraints for refining 3023 atoms. 6200 conditional restraints added. Observations/parameters ratio is 0.36 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2274 (Rfree = 0.000) for 3023 atoms. Found 16 (16 requested) and removed 25 (8 requested) atoms. Cycle 2: After refmac, R = 0.1995 (Rfree = 0.000) for 2973 atoms. Found 6 (16 requested) and removed 13 (8 requested) atoms. Cycle 3: After refmac, R = 0.1919 (Rfree = 0.000) for 2947 atoms. Found 1 (16 requested) and removed 9 (8 requested) atoms. Cycle 4: After refmac, R = 0.1903 (Rfree = 0.000) for 2928 atoms. Found 1 (16 requested) and removed 12 (8 requested) atoms. Failed to save intermediate PDB Cycle 5: After refmac, R = 0.1846 (Rfree = 0.000) for 2911 atoms. Found 3 (16 requested) and removed 11 (8 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.76 4.07 Search for helices and strands: 0 residues in 0 chains, 3033 seeds are put forward NCS extension: 16 residues added (2 deleted due to clashes), 3049 seeds are put forward Round 1: 167 peptides, 32 chains. Longest chain 11 peptides. Score 0.341 Round 2: 203 peptides, 30 chains. Longest chain 23 peptides. Score 0.510 Round 3: 213 peptides, 33 chains. Longest chain 13 peptides. Score 0.499 Round 4: 209 peptides, 28 chains. Longest chain 21 peptides. Score 0.559 Round 5: 224 peptides, 31 chains. Longest chain 17 peptides. Score 0.564 Taking the results from Round 5 Chains 31, Residues 193, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4300 reflections ( 99.54 % complete ) and 7044 restraints for refining 3024 atoms. 6303 conditional restraints added. Observations/parameters ratio is 0.36 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2367 (Rfree = 0.000) for 3024 atoms. Found 7 (16 requested) and removed 18 (8 requested) atoms. Cycle 7: After refmac, R = 0.2179 (Rfree = 0.000) for 3003 atoms. Found 1 (16 requested) and removed 12 (8 requested) atoms. Cycle 8: After refmac, R = 0.2188 (Rfree = 0.000) for 2986 atoms. Found 3 (16 requested) and removed 9 (8 requested) atoms. Failed to save intermediate PDB Cycle 9: After refmac, R = 0.2079 (Rfree = 0.000) for 2973 atoms. Found 1 (16 requested) and removed 8 (8 requested) atoms. Failed to save intermediate PDB Cycle 10: After refmac, R = 0.2010 (Rfree = 0.000) for 2960 atoms. Found 1 (16 requested) and removed 10 (8 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.78 4.10 Search for helices and strands: 0 residues in 0 chains, 3070 seeds are put forward NCS extension: 15 residues added (1 deleted due to clashes), 3085 seeds are put forward Round 1: 182 peptides, 36 chains. Longest chain 12 peptides. Score 0.334 Round 2: 203 peptides, 32 chains. Longest chain 15 peptides. Score 0.480 Round 3: 211 peptides, 28 chains. Longest chain 18 peptides. Score 0.565 Round 4: 207 peptides, 29 chains. Longest chain 27 peptides. Score 0.538 Round 5: 223 peptides, 31 chains. Longest chain 17 peptides. Score 0.561 Taking the results from Round 3 Chains 28, Residues 183, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 4300 reflections ( 99.54 % complete ) and 7018 restraints for refining 3023 atoms. 6314 conditional restraints added. Observations/parameters ratio is 0.36 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2229 (Rfree = 0.000) for 3023 atoms. Found 6 (16 requested) and removed 14 (8 requested) atoms. Failed to save intermediate PDB Cycle 12: After refmac, R = 0.2080 (Rfree = 0.000) for 3006 atoms. Found 3 (16 requested) and removed 9 (8 requested) atoms. Cycle 13: After refmac, R = 0.1898 (Rfree = 0.000) for 2994 atoms. Found 0 (16 requested) and removed 10 (8 requested) atoms. Cycle 14: After refmac, R = 0.1837 (Rfree = 0.000) for 2979 atoms. Found 0 (16 requested) and removed 8 (8 requested) atoms. Cycle 15: After refmac, R = 0.1783 (Rfree = 0.000) for 2965 atoms. Found 2 (16 requested) and removed 10 (8 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.74 4.05 Search for helices and strands: 0 residues in 0 chains, 3071 seeds are put forward NCS extension: 35 residues added (3 deleted due to clashes), 3106 seeds are put forward Round 1: 167 peptides, 31 chains. Longest chain 10 peptides. Score 0.359 Round 2: 187 peptides, 30 chains. Longest chain 15 peptides. Score 0.453 Round 3: 196 peptides, 31 chains. Longest chain 12 peptides. Score 0.470 Round 4: 204 peptides, 33 chains. Longest chain 14 peptides. Score 0.468 Round 5: 199 peptides, 30 chains. Longest chain 18 peptides. Score 0.496 Taking the results from Round 5 Chains 30, Residues 169, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 4300 reflections ( 99.54 % complete ) and 7251 restraints for refining 3024 atoms. 6605 conditional restraints added. Observations/parameters ratio is 0.36 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2055 (Rfree = 0.000) for 3024 atoms. Found 6 (16 requested) and removed 12 (8 requested) atoms. Failed to save intermediate PDB Cycle 17: After refmac, R = 0.1865 (Rfree = 0.000) for 3006 atoms. Found 2 (16 requested) and removed 12 (8 requested) atoms. Failed to save intermediate PDB Cycle 18: After refmac, R = 0.1730 (Rfree = 0.000) for 2993 atoms. Found 1 (16 requested) and removed 9 (8 requested) atoms. Cycle 19: After refmac, R = 0.1849 (Rfree = 0.000) for 2984 atoms. Found 3 (16 requested) and removed 12 (8 requested) atoms. Failed to save intermediate PDB Cycle 20: After refmac, R = 0.1654 (Rfree = 0.000) for 2974 atoms. Found 1 (16 requested) and removed 13 (8 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.72 4.03 Search for helices and strands: 0 residues in 0 chains, 3077 seeds are put forward NCS extension: 17 residues added (2 deleted due to clashes), 3094 seeds are put forward Round 1: 159 peptides, 32 chains. Longest chain 9 peptides. Score 0.308 Round 2: 187 peptides, 31 chains. Longest chain 14 peptides. Score 0.437 Round 3: 198 peptides, 31 chains. Longest chain 15 peptides. Score 0.477 Round 4: 203 peptides, 29 chains. Longest chain 12 peptides. Score 0.525 Round 5: 198 peptides, 27 chains. Longest chain 14 peptides. Score 0.538 Taking the results from Round 5 Chains 27, Residues 171, Estimated correctness of the model 0.0 % 1 chains (7 residues) have been docked in sequence ------------------------------------------------------ 4300 reflections ( 99.54 % complete ) and 7186 restraints for refining 3024 atoms. 6509 conditional restraints added. Observations/parameters ratio is 0.36 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2040 (Rfree = 0.000) for 3024 atoms. Found 9 (16 requested) and removed 9 (8 requested) atoms. Cycle 22: After refmac, R = 0.1863 (Rfree = 0.000) for 3017 atoms. Found 1 (16 requested) and removed 8 (8 requested) atoms. Cycle 23: After refmac, R = 0.1789 (Rfree = 0.000) for 3005 atoms. Found 2 (16 requested) and removed 11 (8 requested) atoms. Cycle 24: After refmac, R = 0.1725 (Rfree = 0.000) for 2991 atoms. Found 1 (16 requested) and removed 8 (8 requested) atoms. Failed to save intermediate PDB Cycle 25: After refmac, R = 0.1665 (Rfree = 0.000) for 2980 atoms. Found 1 (16 requested) and removed 8 (8 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.76 4.07 Search for helices and strands: 0 residues in 0 chains, 3083 seeds are put forward NCS extension: 14 residues added (0 deleted due to clashes), 3097 seeds are put forward Round 1: 154 peptides, 30 chains. Longest chain 11 peptides. Score 0.322 Round 2: 168 peptides, 28 chains. Longest chain 12 peptides. Score 0.414 Round 3: 158 peptides, 28 chains. Longest chain 11 peptides. Score 0.374 Round 4: 178 peptides, 29 chains. Longest chain 15 peptides. Score 0.436 Round 5: 174 peptides, 28 chains. Longest chain 14 peptides. Score 0.437 Taking the results from Round 5 Chains 28, Residues 146, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 4300 reflections ( 99.54 % complete ) and 7364 restraints for refining 3023 atoms. 6808 conditional restraints added. Observations/parameters ratio is 0.36 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2004 (Rfree = 0.000) for 3023 atoms. Found 6 (16 requested) and removed 10 (8 requested) atoms. Cycle 27: After refmac, R = 0.1790 (Rfree = 0.000) for 3013 atoms. Found 1 (16 requested) and removed 11 (8 requested) atoms. Cycle 28: After refmac, R = 0.1707 (Rfree = 0.000) for 3001 atoms. Found 2 (16 requested) and removed 11 (8 requested) atoms. Cycle 29: After refmac, R = 0.1650 (Rfree = 0.000) for 2990 atoms. Found 0 (16 requested) and removed 9 (8 requested) atoms. Cycle 30: After refmac, R = 0.1602 (Rfree = 0.000) for 2980 atoms. Found 2 (16 requested) and removed 8 (8 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.73 4.04 Search for helices and strands: 0 residues in 0 chains, 3099 seeds are put forward NCS extension: 17 residues added (1 deleted due to clashes), 3116 seeds are put forward Round 1: 124 peptides, 25 chains. Longest chain 9 peptides. Score 0.283 Round 2: 150 peptides, 25 chains. Longest chain 11 peptides. Score 0.395 Round 3: 156 peptides, 25 chains. Longest chain 13 peptides. Score 0.418 Round 4: 160 peptides, 24 chains. Longest chain 14 peptides. Score 0.451 Round 5: 160 peptides, 27 chains. Longest chain 9 peptides. Score 0.400 Taking the results from Round 4 Chains 24, Residues 136, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 4300 reflections ( 99.54 % complete ) and 7543 restraints for refining 3023 atoms. 7023 conditional restraints added. Observations/parameters ratio is 0.36 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1827 (Rfree = 0.000) for 3023 atoms. Found 6 (16 requested) and removed 8 (8 requested) atoms. Cycle 32: After refmac, R = 0.1648 (Rfree = 0.000) for 3017 atoms. Found 1 (16 requested) and removed 9 (8 requested) atoms. Cycle 33: After refmac, R = 0.1640 (Rfree = 0.000) for 3005 atoms. Found 1 (16 requested) and removed 9 (8 requested) atoms. Cycle 34: After refmac, R = 0.1520 (Rfree = 0.000) for 2995 atoms. Found 2 (16 requested) and removed 8 (8 requested) atoms. Cycle 35: After refmac, R = 0.1524 (Rfree = 0.000) for 2985 atoms. Found 0 (16 requested) and removed 8 (8 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.72 4.03 Search for helices and strands: 0 residues in 0 chains, 3081 seeds are put forward NCS extension: 6 residues added (0 deleted due to clashes), 3087 seeds are put forward Round 1: 129 peptides, 24 chains. Longest chain 14 peptides. Score 0.325 Round 2: 161 peptides, 28 chains. Longest chain 15 peptides. Score 0.386 Round 3: 153 peptides, 25 chains. Longest chain 16 peptides. Score 0.407 Round 4: 160 peptides, 22 chains. Longest chain 20 peptides. Score 0.484 Round 5: 172 peptides, 24 chains. Longest chain 23 peptides. Score 0.495 Taking the results from Round 5 Chains 24, Residues 148, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 4300 reflections ( 99.54 % complete ) and 7448 restraints for refining 3024 atoms. 6880 conditional restraints added. Observations/parameters ratio is 0.36 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2309 (Rfree = 0.000) for 3024 atoms. Found 16 (16 requested) and removed 9 (8 requested) atoms. Cycle 37: After refmac, R = 0.1952 (Rfree = 0.000) for 3028 atoms. Found 2 (16 requested) and removed 10 (8 requested) atoms. Failed to save intermediate PDB Cycle 38: After refmac, R = 0.1857 (Rfree = 0.000) for 3014 atoms. Found 5 (16 requested) and removed 8 (8 requested) atoms. Failed to save intermediate PDB Cycle 39: After refmac, R = 0.1763 (Rfree = 0.000) for 3004 atoms. Found 1 (16 requested) and removed 9 (8 requested) atoms. Cycle 40: After refmac, R = 0.1729 (Rfree = 0.000) for 2991 atoms. Found 4 (16 requested) and removed 8 (8 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.76 4.07 Search for helices and strands: 0 residues in 0 chains, 3059 seeds are put forward NCS extension: 28 residues added (1 deleted due to clashes), 3087 seeds are put forward Round 1: 122 peptides, 24 chains. Longest chain 12 peptides. Score 0.293 Round 2: 147 peptides, 24 chains. Longest chain 14 peptides. Score 0.400 Round 3: 148 peptides, 23 chains. Longest chain 16 peptides. Score 0.422 Round 4: 150 peptides, 23 chains. Longest chain 15 peptides. Score 0.429 Round 5: 145 peptides, 22 chains. Longest chain 15 peptides. Score 0.427 Taking the results from Round 4 Chains 23, Residues 127, Estimated correctness of the model 0.0 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 4300 reflections ( 99.54 % complete ) and 7422 restraints for refining 3024 atoms. 6902 conditional restraints added. Observations/parameters ratio is 0.36 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1870 (Rfree = 0.000) for 3024 atoms. Found 7 (16 requested) and removed 12 (8 requested) atoms. Failed to save intermediate PDB Cycle 42: After refmac, R = 0.1725 (Rfree = 0.000) for 3006 atoms. Found 2 (16 requested) and removed 9 (8 requested) atoms. Cycle 43: After refmac, R = 0.1685 (Rfree = 0.000) for 2991 atoms. Found 4 (16 requested) and removed 8 (8 requested) atoms. Cycle 44: After refmac, R = 0.1647 (Rfree = 0.000) for 2982 atoms. Found 10 (16 requested) and removed 8 (8 requested) atoms. Cycle 45: After refmac, R = 0.1585 (Rfree = 0.000) for 2980 atoms. Found 3 (16 requested) and removed 10 (8 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.73 4.04 Search for helices and strands: 0 residues in 0 chains, 3048 seeds are put forward NCS extension: 17 residues added (1 deleted due to clashes), 3065 seeds are put forward Round 1: 93 peptides, 19 chains. Longest chain 14 peptides. Score 0.257 Round 2: 113 peptides, 20 chains. Longest chain 14 peptides. Score 0.331 Round 3: 114 peptides, 20 chains. Longest chain 14 peptides. Score 0.335 Round 4: 115 peptides, 19 chains. Longest chain 12 peptides. Score 0.359 Round 5: 128 peptides, 23 chains. Longest chain 9 peptides. Score 0.339 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 19, Residues 96, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence Sequence coverage is 0 % Consider running further cycles of model building using 2fur-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 4300 reflections ( 99.54 % complete ) and 7631 restraints for refining 2998 atoms. 7266 conditional restraints added. Observations/parameters ratio is 0.36 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2036 (Rfree = 0.000) for 2998 atoms. Found 0 (16 requested) and removed 8 (8 requested) atoms. Cycle 47: After refmac, R = 0.1999 (Rfree = 0.000) for 2987 atoms. Found 0 (16 requested) and removed 8 (8 requested) atoms. Cycle 48: After refmac, R = 0.1866 (Rfree = 0.000) for 2977 atoms. Found 0 (16 requested) and removed 8 (8 requested) atoms. Cycle 49: After refmac, R = 0.1796 (Rfree = 0.000) for 2967 atoms. Found 0 (16 requested) and removed 8 (8 requested) atoms. Writing output files ... Failed to save intermediate PDB Normal termination of warpNtrace Tue 25 Dec 20:21:06 GMT 2018 Job finished. TimeTaking 53.16