null Sun 23 Dec 22:23:10 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 2gpj-3.8-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2gpj-3.8-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2gpj-3.8-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2gpj-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/2gpj-3.8-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2gpj-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 ============================================================ Sun 23 Dec 22:23:19 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/2gpj-3.8-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2gpj-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 217 and 0 Target number of residues in the AU: 217 Target solvent content: 0.6558 Checking the provided sequence file Detected sequence length: 252 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 1 Adjusted target number of residues: 252 Adjusted target solvent content: 0.60 Input MTZ file: 2gpj-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: 92 Cell parameters: 100.540 100.540 67.510 90.000 90.000 90.000 Input sequence file: 2gpj-3.8-parrot-hancs.fasta_lf Building free atoms model in initial map for 2016 target number of atoms Had to go as low as 0.75 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 Loops will be built when appropriate and at the last cycle Resolution range: 71.093 3.800 Wilson plot Bfac: 82.02 3682 reflections ( 99.38 % complete ) and 0 restraints for refining 2228 atoms. Observations/parameters ratio is 0.41 ------------------------------------------------------ Starting model: R = 0.3948 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3828 (Rfree = 0.000) for 2228 atoms. Found 12 (12 requested) and removed 26 (6 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.61 3.15 Search for helices and strands: 0 residues in 0 chains, 2242 seeds are put forward Round 1: 95 peptides, 20 chains. Longest chain 8 peptides. Score 0.256 Round 2: 96 peptides, 19 chains. Longest chain 8 peptides. Score 0.285 Round 3: 107 peptides, 18 chains. Longest chain 11 peptides. Score 0.366 Round 4: 115 peptides, 18 chains. Longest chain 12 peptides. Score 0.406 Round 5: 117 peptides, 20 chains. Longest chain 12 peptides. Score 0.372 Taking the results from Round 4 Chains 18, Residues 97, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3682 reflections ( 99.38 % complete ) and 4314 restraints for refining 1824 atoms. 3944 conditional restraints added. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3057 (Rfree = 0.000) for 1824 atoms. Found 8 (10 requested) and removed 11 (5 requested) atoms. Cycle 2: After refmac, R = 0.2914 (Rfree = 0.000) for 1804 atoms. Found 2 (10 requested) and removed 9 (5 requested) atoms. Cycle 3: After refmac, R = 0.2796 (Rfree = 0.000) for 1793 atoms. Found 0 (9 requested) and removed 7 (4 requested) atoms. Cycle 4: After refmac, R = 0.2767 (Rfree = 0.000) for 1780 atoms. Found 1 (9 requested) and removed 8 (4 requested) atoms. Cycle 5: After refmac, R = 0.2680 (Rfree = 0.000) for 1773 atoms. Found 0 (9 requested) and removed 8 (4 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.68 3.22 Search for helices and strands: 0 residues in 0 chains, 1820 seeds are put forward Round 1: 111 peptides, 21 chains. Longest chain 11 peptides. Score 0.320 Round 2: 113 peptides, 20 chains. Longest chain 10 peptides. Score 0.352 Round 3: 125 peptides, 21 chains. Longest chain 12 peptides. Score 0.390 Round 4: 109 peptides, 18 chains. Longest chain 10 peptides. Score 0.376 Round 5: 121 peptides, 20 chains. Longest chain 14 peptides. Score 0.392 Taking the results from Round 5 Chains 20, Residues 101, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3682 reflections ( 99.38 % complete ) and 4372 restraints for refining 1824 atoms. 3988 conditional restraints added. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2929 (Rfree = 0.000) for 1824 atoms. Found 5 (10 requested) and removed 6 (5 requested) atoms. Cycle 7: After refmac, R = 0.2747 (Rfree = 0.000) for 1804 atoms. Found 2 (10 requested) and removed 6 (5 requested) atoms. Cycle 8: After refmac, R = 0.2653 (Rfree = 0.000) for 1789 atoms. Found 0 (9 requested) and removed 5 (4 requested) atoms. Cycle 9: After refmac, R = 0.2648 (Rfree = 0.000) for 1776 atoms. Found 3 (9 requested) and removed 4 (4 requested) atoms. Cycle 10: After refmac, R = 0.2593 (Rfree = 0.000) for 1770 atoms. Found 3 (9 requested) and removed 5 (4 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.68 3.22 Search for helices and strands: 0 residues in 0 chains, 1805 seeds are put forward Round 1: 117 peptides, 25 chains. Longest chain 9 peptides. Score 0.262 Round 2: 126 peptides, 23 chains. Longest chain 11 peptides. Score 0.353 Round 3: 117 peptides, 22 chains. Longest chain 10 peptides. Score 0.329 Round 4: 110 peptides, 20 chains. Longest chain 9 peptides. Score 0.337 Round 5: 117 peptides, 20 chains. Longest chain 13 peptides. Score 0.372 Taking the results from Round 5 Chains 21, Residues 97, Estimated correctness of the model 0.0 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 3682 reflections ( 99.38 % complete ) and 4257 restraints for refining 1824 atoms. 3858 conditional restraints added. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2835 (Rfree = 0.000) for 1824 atoms. Found 5 (10 requested) and removed 7 (5 requested) atoms. Cycle 12: After refmac, R = 0.2702 (Rfree = 0.000) for 1810 atoms. Found 2 (10 requested) and removed 5 (5 requested) atoms. Cycle 13: After refmac, R = 0.2719 (Rfree = 0.000) for 1798 atoms. Found 1 (9 requested) and removed 4 (4 requested) atoms. Cycle 14: After refmac, R = 0.2650 (Rfree = 0.000) for 1794 atoms. Found 4 (9 requested) and removed 4 (4 requested) atoms. Cycle 15: After refmac, R = 0.2625 (Rfree = 0.000) for 1794 atoms. Found 2 (9 requested) and removed 5 (4 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.70 3.23 Search for helices and strands: 0 residues in 0 chains, 1826 seeds are put forward Round 1: 113 peptides, 21 chains. Longest chain 10 peptides. Score 0.330 Round 2: 123 peptides, 21 chains. Longest chain 12 peptides. Score 0.380 Round 3: 124 peptides, 21 chains. Longest chain 16 peptides. Score 0.385 Round 4: 117 peptides, 20 chains. Longest chain 16 peptides. Score 0.372 Round 5: 116 peptides, 20 chains. Longest chain 10 peptides. Score 0.367 Taking the results from Round 3 Chains 21, Residues 103, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3682 reflections ( 99.38 % complete ) and 4302 restraints for refining 1824 atoms. 3911 conditional restraints added. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2989 (Rfree = 0.000) for 1824 atoms. Found 7 (10 requested) and removed 5 (5 requested) atoms. Cycle 17: After refmac, R = 0.2818 (Rfree = 0.000) for 1811 atoms. Found 10 (10 requested) and removed 5 (5 requested) atoms. Cycle 18: After refmac, R = 0.2787 (Rfree = 0.000) for 1807 atoms. Found 1 (9 requested) and removed 4 (4 requested) atoms. Cycle 19: After refmac, R = 0.2772 (Rfree = 0.000) for 1800 atoms. Found 3 (9 requested) and removed 6 (4 requested) atoms. Cycle 20: After refmac, R = 0.2765 (Rfree = 0.000) for 1796 atoms. Found 2 (9 requested) and removed 4 (4 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.65 3.19 Search for helices and strands: 0 residues in 0 chains, 1823 seeds are put forward Round 1: 101 peptides, 21 chains. Longest chain 9 peptides. Score 0.266 Round 2: 115 peptides, 21 chains. Longest chain 9 peptides. Score 0.340 Round 3: 125 peptides, 22 chains. Longest chain 11 peptides. Score 0.369 Round 4: 119 peptides, 21 chains. Longest chain 13 peptides. Score 0.361 Round 5: 107 peptides, 17 chains. Longest chain 11 peptides. Score 0.388 Taking the results from Round 5 Chains 17, Residues 90, Estimated correctness of the model 0.0 % 2 chains (12 residues) have been docked in sequence ------------------------------------------------------ 3682 reflections ( 99.38 % complete ) and 4246 restraints for refining 1823 atoms. 3872 conditional restraints added. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2916 (Rfree = 0.000) for 1823 atoms. Found 8 (10 requested) and removed 7 (5 requested) atoms. Cycle 22: After refmac, R = 0.2808 (Rfree = 0.000) for 1823 atoms. Found 3 (10 requested) and removed 6 (5 requested) atoms. Cycle 23: After refmac, R = 0.2786 (Rfree = 0.000) for 1818 atoms. Found 1 (10 requested) and removed 5 (5 requested) atoms. Cycle 24: After refmac, R = 0.2781 (Rfree = 0.000) for 1811 atoms. Found 3 (9 requested) and removed 5 (4 requested) atoms. Cycle 25: After refmac, R = 0.2766 (Rfree = 0.000) for 1809 atoms. Found 0 (9 requested) and removed 4 (4 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.65 3.19 Search for helices and strands: 0 residues in 0 chains, 1829 seeds are put forward Round 1: 107 peptides, 19 chains. Longest chain 10 peptides. Score 0.344 Round 2: 112 peptides, 19 chains. Longest chain 12 peptides. Score 0.369 Round 3: 104 peptides, 16 chains. Longest chain 13 peptides. Score 0.396 Round 4: 102 peptides, 17 chains. Longest chain 10 peptides. Score 0.363 Round 5: 97 peptides, 15 chains. Longest chain 12 peptides. Score 0.383 Taking the results from Round 3 Chains 16, Residues 88, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3682 reflections ( 99.38 % complete ) and 4376 restraints for refining 1824 atoms. 4040 conditional restraints added. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2950 (Rfree = 0.000) for 1824 atoms. Found 6 (10 requested) and removed 5 (5 requested) atoms. Cycle 27: After refmac, R = 0.2862 (Rfree = 0.000) for 1818 atoms. Found 5 (10 requested) and removed 5 (5 requested) atoms. Cycle 28: After refmac, R = 0.2780 (Rfree = 0.000) for 1817 atoms. Found 2 (9 requested) and removed 4 (4 requested) atoms. Cycle 29: After refmac, R = 0.2747 (Rfree = 0.000) for 1814 atoms. Found 1 (9 requested) and removed 4 (4 requested) atoms. Cycle 30: After refmac, R = 0.2669 (Rfree = 0.000) for 1808 atoms. Found 0 (9 requested) and removed 4 (4 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.68 3.22 Search for helices and strands: 0 residues in 0 chains, 1826 seeds are put forward Round 1: 103 peptides, 21 chains. Longest chain 8 peptides. Score 0.277 Round 2: 100 peptides, 19 chains. Longest chain 8 peptides. Score 0.307 Round 3: 103 peptides, 19 chains. Longest chain 8 peptides. Score 0.323 Round 4: 107 peptides, 19 chains. Longest chain 10 peptides. Score 0.344 Round 5: 109 peptides, 20 chains. Longest chain 11 peptides. Score 0.332 Taking the results from Round 4 Chains 19, Residues 88, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3682 reflections ( 99.38 % complete ) and 4322 restraints for refining 1823 atoms. 3989 conditional restraints added. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2934 (Rfree = 0.000) for 1823 atoms. Found 8 (10 requested) and removed 7 (5 requested) atoms. Cycle 32: After refmac, R = 0.2828 (Rfree = 0.000) for 1820 atoms. Found 2 (10 requested) and removed 6 (5 requested) atoms. Cycle 33: After refmac, R = 0.2719 (Rfree = 0.000) for 1812 atoms. Found 1 (9 requested) and removed 4 (4 requested) atoms. Cycle 34: After refmac, R = 0.2880 (Rfree = 0.000) for 1807 atoms. Found 1 (9 requested) and removed 5 (4 requested) atoms. Cycle 35: After refmac, R = 0.2640 (Rfree = 0.000) for 1801 atoms. Found 1 (9 requested) and removed 6 (4 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.68 3.22 Search for helices and strands: 0 residues in 0 chains, 1824 seeds are put forward Round 1: 89 peptides, 17 chains. Longest chain 10 peptides. Score 0.294 Round 2: 96 peptides, 16 chains. Longest chain 11 peptides. Score 0.355 Round 3: 104 peptides, 20 chains. Longest chain 11 peptides. Score 0.305 Round 4: 95 peptides, 15 chains. Longest chain 15 peptides. Score 0.373 Round 5: 90 peptides, 16 chains. Longest chain 11 peptides. Score 0.323 Taking the results from Round 4 Chains 15, Residues 80, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3682 reflections ( 99.38 % complete ) and 4478 restraints for refining 1823 atoms. 4173 conditional restraints added. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2869 (Rfree = 0.000) for 1823 atoms. Found 7 (10 requested) and removed 5 (5 requested) atoms. Cycle 37: After refmac, R = 0.2965 (Rfree = 0.000) for 1824 atoms. Found 4 (10 requested) and removed 5 (5 requested) atoms. Cycle 38: After refmac, R = 0.3434 (Rfree = 0.000) for 1821 atoms. Found 9 (10 requested) and removed 5 (5 requested) atoms. Cycle 39: After refmac, R = 0.2827 (Rfree = 0.000) for 1820 atoms. Found 4 (10 requested) and removed 5 (5 requested) atoms. Cycle 40: After refmac, R = 0.2745 (Rfree = 0.000) for 1817 atoms. Found 8 (10 requested) and removed 5 (5 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.66 3.20 Search for helices and strands: 0 residues in 0 chains, 1840 seeds are put forward Round 1: 94 peptides, 20 chains. Longest chain 7 peptides. Score 0.250 Round 2: 99 peptides, 20 chains. Longest chain 10 peptides. Score 0.278 Round 3: 96 peptides, 16 chains. Longest chain 13 peptides. Score 0.355 Round 4: 94 peptides, 16 chains. Longest chain 10 peptides. Score 0.345 Round 5: 89 peptides, 16 chains. Longest chain 11 peptides. Score 0.318 Taking the results from Round 3 Chains 16, Residues 80, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3682 reflections ( 99.38 % complete ) and 4509 restraints for refining 1823 atoms. 4205 conditional restraints added. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2767 (Rfree = 0.000) for 1823 atoms. Found 9 (10 requested) and removed 6 (5 requested) atoms. Cycle 42: After refmac, R = 0.3430 (Rfree = 0.000) for 1821 atoms. Found 10 (10 requested) and removed 6 (5 requested) atoms. Cycle 43: After refmac, R = 0.2653 (Rfree = 0.000) for 1821 atoms. Found 10 (10 requested) and removed 6 (5 requested) atoms. Cycle 44: After refmac, R = 0.2618 (Rfree = 0.000) for 1824 atoms. Found 10 (10 requested) and removed 7 (5 requested) atoms. Cycle 45: After refmac, R = 0.2631 (Rfree = 0.000) for 1819 atoms. Found 10 (10 requested) and removed 6 (5 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.63 3.17 Search for helices and strands: 0 residues in 0 chains, 1855 seeds are put forward Round 1: 93 peptides, 20 chains. Longest chain 7 peptides. Score 0.244 Round 2: 92 peptides, 17 chains. Longest chain 11 peptides. Score 0.310 Round 3: 94 peptides, 16 chains. Longest chain 11 peptides. Score 0.345 Round 4: 89 peptides, 15 chains. Longest chain 8 peptides. Score 0.342 Round 5: 96 peptides, 16 chains. Longest chain 11 peptides. Score 0.355 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 16, Residues 80, Estimated correctness of the model 0.0 % 2 chains (18 residues) have been docked in sequence Sequence coverage is 22 % Consider running further cycles of model building using 2gpj-3_warpNtrace.pdb as input Building loops using Loopy2018 16 chains (80 residues) following loop building 2 chains (18 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 3682 reflections ( 99.38 % complete ) and 4212 restraints for refining 1823 atoms. 3841 conditional restraints added. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2980 (Rfree = 0.000) for 1823 atoms. Found 0 (10 requested) and removed 5 (5 requested) atoms. Cycle 47: After refmac, R = 0.2744 (Rfree = 0.000) for 1812 atoms. Found 0 (9 requested) and removed 4 (4 requested) atoms. Cycle 48: After refmac, R = 0.2623 (Rfree = 0.000) for 1799 atoms. Found 0 (9 requested) and removed 4 (4 requested) atoms. Cycle 49: After refmac, R = 0.2593 (Rfree = 0.000) for 1782 atoms. Found 0 (9 requested) and removed 4 (4 requested) atoms. Writing output files ... Normal termination of warpNtrace Sun 23 Dec 22:56:13 GMT 2018 Job finished. TimeTaking 33.05 Used memory is bytes: 8699984