null Mon 24 Dec 07:51:38 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir Job ID is set to 2fur-3.4-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/2fur-3.4-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/2fur-3.4-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2fur-3.4-parrot-noncs 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/noncs/ArpWArp/wArpResults/WorkingDir/2fur-3.4-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2fur-3.4-parrot-noncs ############### 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 ============================================================ Mon 24 Dec 07:51:42 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/noncs/ArpWArp/wArpResults/WorkingDir/2fur-3.4-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2fur-3.4-parrot-noncs/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 265 and 0 Target number of residues in the AU: 265 Target solvent content: 0.6475 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-3.4-parrot-noncs.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-3.4-parrot-noncs.fasta_lf Building free atoms model in initial map for 3344 target number of atoms Had to go as low as 0.65 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 3.400 Wilson plot Bfac: 76.06 5955 reflections ( 99.65 % complete ) and 0 restraints for refining 3724 atoms. Observations/parameters ratio is 0.40 ------------------------------------------------------ Starting model: R = 0.3272 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3018 (Rfree = 0.000) for 3724 atoms. Found 11 (28 requested) and removed 45 (14 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.43 3.72 Search for helices and strands: 0 residues in 0 chains, 3745 seeds are put forward NCS extension: 0 residues added, 3745 seeds are put forward Round 1: 191 peptides, 36 chains. Longest chain 13 peptides. Score 0.370 Round 2: 232 peptides, 32 chains. Longest chain 19 peptides. Score 0.575 Round 3: 239 peptides, 31 chains. Longest chain 24 peptides. Score 0.609 Round 4: 251 peptides, 28 chains. Longest chain 25 peptides. Score 0.677 Round 5: 267 peptides, 26 chains. Longest chain 31 peptides. Score 0.733 Taking the results from Round 5 Chains 27, Residues 241, Estimated correctness of the model 66.0 % 4 chains (70 residues) have been docked in sequence Building loops using Loopy2018 27 chains (241 residues) following loop building 4 chains (70 residues) in sequence following loop building ------------------------------------------------------ 5955 reflections ( 99.65 % complete ) and 6002 restraints for refining 3039 atoms. 4795 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2536 (Rfree = 0.000) for 3039 atoms. Found 10 (22 requested) and removed 31 (11 requested) atoms. Cycle 2: After refmac, R = 0.2349 (Rfree = 0.000) for 2974 atoms. Found 6 (22 requested) and removed 19 (11 requested) atoms. Cycle 3: After refmac, R = 0.2256 (Rfree = 0.000) for 2943 atoms. Found 4 (21 requested) and removed 23 (11 requested) atoms. Cycle 4: After refmac, R = 0.2232 (Rfree = 0.000) for 2922 atoms. Found 2 (21 requested) and removed 16 (11 requested) atoms. Cycle 5: After refmac, R = 0.2112 (Rfree = 0.000) for 2907 atoms. Found 1 (19 requested) and removed 10 (10 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.41 3.70 Search for helices and strands: 0 residues in 0 chains, 3009 seeds are put forward NCS extension: 25 residues added (11 deleted due to clashes), 3034 seeds are put forward Round 1: 211 peptides, 32 chains. Longest chain 23 peptides. Score 0.507 Round 2: 245 peptides, 33 chains. Longest chain 24 peptides. Score 0.601 Round 3: 246 peptides, 30 chains. Longest chain 24 peptides. Score 0.641 Round 4: 251 peptides, 30 chains. Longest chain 24 peptides. Score 0.654 Round 5: 235 peptides, 30 chains. Longest chain 19 peptides. Score 0.610 Taking the results from Round 4 Chains 31, Residues 221, Estimated correctness of the model 45.3 % 2 chains (27 residues) have been docked in sequence ------------------------------------------------------ 5955 reflections ( 99.65 % complete ) and 6630 restraints for refining 3041 atoms. 5669 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2319 (Rfree = 0.000) for 3041 atoms. Found 16 (20 requested) and removed 26 (11 requested) atoms. Cycle 7: After refmac, R = 0.2103 (Rfree = 0.000) for 3022 atoms. Found 5 (20 requested) and removed 17 (11 requested) atoms. Cycle 8: After refmac, R = 0.1991 (Rfree = 0.000) for 3004 atoms. Found 1 (20 requested) and removed 12 (11 requested) atoms. Cycle 9: After refmac, R = 0.1928 (Rfree = 0.000) for 2991 atoms. Found 3 (20 requested) and removed 11 (11 requested) atoms. Cycle 10: After refmac, R = 0.1843 (Rfree = 0.000) for 2982 atoms. Found 0 (20 requested) and removed 11 (11 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.36 3.64 Search for helices and strands: 0 residues in 0 chains, 3067 seeds are put forward NCS extension: 23 residues added (2 deleted due to clashes), 3090 seeds are put forward Round 1: 199 peptides, 29 chains. Longest chain 18 peptides. Score 0.511 Round 2: 219 peptides, 28 chains. Longest chain 24 peptides. Score 0.590 Round 3: 228 peptides, 30 chains. Longest chain 24 peptides. Score 0.590 Round 4: 232 peptides, 31 chains. Longest chain 26 peptides. Score 0.589 Round 5: 233 peptides, 31 chains. Longest chain 29 peptides. Score 0.592 Taking the results from Round 5 Chains 33, Residues 202, Estimated correctness of the model 26.0 % 1 chains (13 residues) have been docked in sequence ------------------------------------------------------ 5955 reflections ( 99.65 % complete ) and 6813 restraints for refining 3039 atoms. 5979 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2076 (Rfree = 0.000) for 3039 atoms. Found 9 (20 requested) and removed 16 (11 requested) atoms. Cycle 12: After refmac, R = 0.1988 (Rfree = 0.000) for 3017 atoms. Found 5 (20 requested) and removed 18 (11 requested) atoms. Cycle 13: After refmac, R = 0.1888 (Rfree = 0.000) for 2997 atoms. Found 3 (20 requested) and removed 13 (11 requested) atoms. Cycle 14: After refmac, R = 0.1740 (Rfree = 0.000) for 2985 atoms. Found 2 (20 requested) and removed 12 (11 requested) atoms. Cycle 15: After refmac, R = 0.1694 (Rfree = 0.000) for 2973 atoms. Found 6 (20 requested) and removed 13 (11 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.37 3.65 Search for helices and strands: 0 residues in 0 chains, 3048 seeds are put forward NCS extension: 14 residues added (4 deleted due to clashes), 3062 seeds are put forward Round 1: 192 peptides, 32 chains. Longest chain 13 peptides. Score 0.440 Round 2: 225 peptides, 30 chains. Longest chain 17 peptides. Score 0.581 Round 3: 213 peptides, 30 chains. Longest chain 17 peptides. Score 0.543 Round 4: 223 peptides, 31 chains. Longest chain 15 peptides. Score 0.561 Round 5: 234 peptides, 32 chains. Longest chain 18 peptides. Score 0.581 Taking the results from Round 5 Chains 32, Residues 202, Estimated correctness of the model 22.4 % 2 chains (21 residues) have been docked in sequence ------------------------------------------------------ 5955 reflections ( 99.65 % complete ) and 6647 restraints for refining 3040 atoms. 5789 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2021 (Rfree = 0.000) for 3040 atoms. Found 8 (20 requested) and removed 16 (11 requested) atoms. Cycle 17: After refmac, R = 0.1860 (Rfree = 0.000) for 3018 atoms. Found 4 (20 requested) and removed 12 (11 requested) atoms. Cycle 18: After refmac, R = 0.1826 (Rfree = 0.000) for 3003 atoms. Found 4 (20 requested) and removed 12 (11 requested) atoms. Cycle 19: After refmac, R = 0.1898 (Rfree = 0.000) for 2987 atoms. Found 7 (20 requested) and removed 13 (11 requested) atoms. Cycle 20: After refmac, R = 0.1777 (Rfree = 0.000) for 2977 atoms. Found 3 (20 requested) and removed 15 (11 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.34 3.62 Search for helices and strands: 0 residues in 0 chains, 3066 seeds are put forward NCS extension: 29 residues added (2 deleted due to clashes), 3095 seeds are put forward Round 1: 205 peptides, 34 chains. Longest chain 18 peptides. Score 0.456 Round 2: 233 peptides, 30 chains. Longest chain 18 peptides. Score 0.604 Round 3: 224 peptides, 28 chains. Longest chain 20 peptides. Score 0.605 Round 4: 225 peptides, 29 chains. Longest chain 16 peptides. Score 0.594 Round 5: 226 peptides, 30 chains. Longest chain 19 peptides. Score 0.584 Taking the results from Round 3 Chains 28, Residues 196, Estimated correctness of the model 30.3 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5955 reflections ( 99.65 % complete ) and 6908 restraints for refining 3040 atoms. 6152 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2055 (Rfree = 0.000) for 3040 atoms. Found 12 (20 requested) and removed 25 (11 requested) atoms. Cycle 22: After refmac, R = 0.2044 (Rfree = 0.000) for 3019 atoms. Found 16 (20 requested) and removed 14 (11 requested) atoms. Cycle 23: After refmac, R = 0.1978 (Rfree = 0.000) for 3012 atoms. Found 8 (20 requested) and removed 14 (11 requested) atoms. Cycle 24: After refmac, R = 0.1891 (Rfree = 0.000) for 2998 atoms. Found 4 (20 requested) and removed 12 (11 requested) atoms. Cycle 25: After refmac, R = 0.1945 (Rfree = 0.000) for 2987 atoms. Found 9 (20 requested) and removed 15 (11 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.36 3.64 Search for helices and strands: 0 residues in 0 chains, 3089 seeds are put forward NCS extension: 18 residues added (0 deleted due to clashes), 3107 seeds are put forward Round 1: 189 peptides, 31 chains. Longest chain 14 peptides. Score 0.445 Round 2: 212 peptides, 32 chains. Longest chain 13 peptides. Score 0.511 Round 3: 208 peptides, 26 chains. Longest chain 21 peptides. Score 0.584 Round 4: 233 peptides, 29 chains. Longest chain 16 peptides. Score 0.617 Round 5: 212 peptides, 26 chains. Longest chain 23 peptides. Score 0.596 Taking the results from Round 4 Chains 29, Residues 204, Estimated correctness of the model 34.1 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5955 reflections ( 99.65 % complete ) and 6914 restraints for refining 3041 atoms. 6127 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2049 (Rfree = 0.000) for 3041 atoms. Found 8 (20 requested) and removed 13 (11 requested) atoms. Cycle 27: After refmac, R = 0.2016 (Rfree = 0.000) for 3029 atoms. Found 5 (20 requested) and removed 15 (11 requested) atoms. Cycle 28: After refmac, R = 0.1755 (Rfree = 0.000) for 3017 atoms. Found 3 (20 requested) and removed 13 (11 requested) atoms. Cycle 29: After refmac, R = 0.1741 (Rfree = 0.000) for 3003 atoms. Found 0 (20 requested) and removed 11 (11 requested) atoms. Cycle 30: After refmac, R = 0.1731 (Rfree = 0.000) for 2991 atoms. Found 2 (20 requested) and removed 11 (11 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.40 3.68 Search for helices and strands: 0 residues in 0 chains, 3073 seeds are put forward NCS extension: 13 residues added (2 deleted due to clashes), 3086 seeds are put forward Round 1: 199 peptides, 31 chains. Longest chain 15 peptides. Score 0.481 Round 2: 222 peptides, 28 chains. Longest chain 27 peptides. Score 0.599 Round 3: 220 peptides, 29 chains. Longest chain 23 peptides. Score 0.579 Round 4: 216 peptides, 27 chains. Longest chain 22 peptides. Score 0.594 Round 5: 211 peptides, 27 chains. Longest chain 18 peptides. Score 0.579 Taking the results from Round 2 Chains 28, Residues 194, Estimated correctness of the model 28.3 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5955 reflections ( 99.65 % complete ) and 6815 restraints for refining 3040 atoms. 6067 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1921 (Rfree = 0.000) for 3040 atoms. Found 7 (20 requested) and removed 11 (11 requested) atoms. Cycle 32: After refmac, R = 0.1896 (Rfree = 0.000) for 3035 atoms. Found 5 (20 requested) and removed 15 (11 requested) atoms. Cycle 33: After refmac, R = 0.1855 (Rfree = 0.000) for 3020 atoms. Found 2 (20 requested) and removed 13 (11 requested) atoms. Cycle 34: After refmac, R = 0.1607 (Rfree = 0.000) for 3006 atoms. Found 3 (20 requested) and removed 11 (11 requested) atoms. Cycle 35: After refmac, R = 0.1650 (Rfree = 0.000) for 2996 atoms. Found 3 (20 requested) and removed 11 (11 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.40 3.68 Search for helices and strands: 0 residues in 0 chains, 3086 seeds are put forward NCS extension: 42 residues added (0 deleted due to clashes), 3128 seeds are put forward Round 1: 188 peptides, 31 chains. Longest chain 12 peptides. Score 0.441 Round 2: 220 peptides, 24 chains. Longest chain 27 peptides. Score 0.644 Round 3: 235 peptides, 27 chains. Longest chain 31 peptides. Score 0.648 Round 4: 219 peptides, 30 chains. Longest chain 14 peptides. Score 0.562 Round 5: 240 peptides, 29 chains. Longest chain 20 peptides. Score 0.637 Taking the results from Round 3 Chains 27, Residues 208, Estimated correctness of the model 43.6 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5955 reflections ( 99.65 % complete ) and 6726 restraints for refining 3041 atoms. 5921 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1826 (Rfree = 0.000) for 3041 atoms. Found 6 (20 requested) and removed 12 (11 requested) atoms. Cycle 37: After refmac, R = 0.1810 (Rfree = 0.000) for 3030 atoms. Found 7 (20 requested) and removed 13 (11 requested) atoms. Cycle 38: After refmac, R = 0.1722 (Rfree = 0.000) for 3020 atoms. Found 4 (20 requested) and removed 12 (11 requested) atoms. Cycle 39: After refmac, R = 0.1604 (Rfree = 0.000) for 3003 atoms. Found 6 (20 requested) and removed 13 (11 requested) atoms. Cycle 40: After refmac, R = 0.1548 (Rfree = 0.000) for 2992 atoms. Found 3 (20 requested) and removed 11 (11 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.40 3.68 Search for helices and strands: 0 residues in 0 chains, 3079 seeds are put forward NCS extension: 34 residues added (1 deleted due to clashes), 3113 seeds are put forward Round 1: 183 peptides, 34 chains. Longest chain 13 peptides. Score 0.372 Round 2: 189 peptides, 27 chains. Longest chain 15 peptides. Score 0.507 Round 3: 199 peptides, 28 chains. Longest chain 13 peptides. Score 0.526 Round 4: 206 peptides, 32 chains. Longest chain 17 peptides. Score 0.490 Round 5: 196 peptides, 29 chains. Longest chain 22 peptides. Score 0.501 Taking the results from Round 3 Chains 28, Residues 171, Estimated correctness of the model 2.7 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5955 reflections ( 99.65 % complete ) and 7002 restraints for refining 3041 atoms. 6346 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1811 (Rfree = 0.000) for 3041 atoms. Found 18 (20 requested) and removed 12 (11 requested) atoms. Cycle 42: After refmac, R = 0.1828 (Rfree = 0.000) for 3044 atoms. Found 10 (21 requested) and removed 11 (11 requested) atoms. Cycle 43: After refmac, R = 0.1768 (Rfree = 0.000) for 3036 atoms. Found 16 (20 requested) and removed 13 (11 requested) atoms. Cycle 44: After refmac, R = 0.1724 (Rfree = 0.000) for 3034 atoms. Found 17 (20 requested) and removed 12 (11 requested) atoms. Cycle 45: After refmac, R = 0.1660 (Rfree = 0.000) for 3037 atoms. Found 15 (20 requested) and removed 11 (11 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.37 3.65 Search for helices and strands: 0 residues in 0 chains, 3124 seeds are put forward NCS extension: 16 residues added (0 deleted due to clashes), 3140 seeds are put forward Round 1: 150 peptides, 26 chains. Longest chain 12 peptides. Score 0.377 Round 2: 158 peptides, 25 chains. Longest chain 14 peptides. Score 0.426 Round 3: 179 peptides, 24 chains. Longest chain 15 peptides. Score 0.519 Round 4: 186 peptides, 26 chains. Longest chain 15 peptides. Score 0.512 Round 5: 191 peptides, 25 chains. Longest chain 16 peptides. Score 0.544 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 25, Residues 166, Estimated correctness of the model 9.3 % 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. 5955 reflections ( 99.65 % complete ) and 7020 restraints for refining 3041 atoms. 6381 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1935 (Rfree = 0.000) for 3041 atoms. Found 0 (20 requested) and removed 11 (11 requested) atoms. Cycle 47: After refmac, R = 0.1797 (Rfree = 0.000) for 3024 atoms. Found 0 (20 requested) and removed 11 (11 requested) atoms. Cycle 48: After refmac, R = 0.1795 (Rfree = 0.000) for 3012 atoms. Found 0 (20 requested) and removed 11 (11 requested) atoms. Cycle 49: After refmac, R = 0.1679 (Rfree = 0.000) for 2996 atoms. Found 0 (20 requested) and removed 11 (11 requested) atoms. Writing output files ... Normal termination of warpNtrace Mon 24 Dec 08:26:54 GMT 2018 Job finished. TimeTaking 35.26 Used memory is bytes: 13379496