Mon 24 Dec 07:31:55 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 2p10-4.0-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/2p10-4.0-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/2p10-4.0-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2p10-4.0-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/2p10-4.0-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2p10-4.0-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 07:31:59 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/2p10-4.0-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2p10-4.0-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 1409 and 0 Target number of residues in the AU: 1409 Target solvent content: 0.6714 Checking the provided sequence file Detected sequence length: 286 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 6 Adjusted target number of residues: 1716 Adjusted target solvent content: 0.60 Input MTZ file: 2p10-4.0-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: 146 Cell parameters: 180.269 180.269 185.514 90.000 90.000 120.000 Input sequence file: 2p10-4.0-parrot-noncs.fasta_lf Building free atoms model in initial map for 13728 target number of atoms Had to go as low as 0.90 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: 119.449 4.001 Wilson plot Bfac: 93.52 *** WARNING *** *** WARNING *** This resolution is too low for ARP/wARP protein chain tracing *** WARNING *** Failed to save intermediate PDB 18377 reflections ( 96.69 % complete ) and 0 restraints for refining 15152 atoms. Observations/parameters ratio is 0.30 ------------------------------------------------------ Starting model: R = 0.3167 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3017 (Rfree = 0.000) for 15152 atoms. Found 71 (71 requested) and removed 381 (35 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.86 3.37 Search for helices and strands: 0 residues in 0 chains, 15113 seeds are put forward NCS extension: 0 residues added, 15113 seeds are put forward Round 1: 612 peptides, 117 chains. Longest chain 12 peptides. Score 0.294 Round 2: 762 peptides, 110 chains. Longest chain 18 peptides. Score 0.430 Round 3: 836 peptides, 112 chains. Longest chain 25 peptides. Score 0.474 Round 4: 862 peptides, 109 chains. Longest chain 26 peptides. Score 0.499 Round 5: 852 peptides, 103 chains. Longest chain 22 peptides. Score 0.510 Taking the results from Round 5 Chains 117, Residues 749, Estimated correctness of the model 0.0 % 26 chains (216 residues) have been docked in sequence ------------------------------------------------------ 18377 reflections ( 96.69 % complete ) and 27300 restraints for refining 12248 atoms. 23883 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2335 (Rfree = 0.000) for 12248 atoms. Found 58 (58 requested) and removed 144 (29 requested) atoms. Cycle 2: After refmac, R = 0.2106 (Rfree = 0.000) for 11890 atoms. Found 57 (57 requested) and removed 91 (28 requested) atoms. Cycle 3: After refmac, R = 0.1963 (Rfree = 0.000) for 11741 atoms. Found 54 (56 requested) and removed 72 (28 requested) atoms. Cycle 4: After refmac, R = 0.1862 (Rfree = 0.000) for 11659 atoms. Found 39 (55 requested) and removed 68 (27 requested) atoms. Failed to save intermediate PDB Cycle 5: After refmac, R = 0.1854 (Rfree = 0.000) for 11574 atoms. Found 44 (55 requested) and removed 60 (27 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.85 3.36 Search for helices and strands: 0 residues in 0 chains, 12000 seeds are put forward NCS extension: 16 residues added (0 deleted due to clashes), 12016 seeds are put forward Round 1: 788 peptides, 123 chains. Longest chain 17 peptides. Score 0.408 Round 2: 862 peptides, 103 chains. Longest chain 23 peptides. Score 0.517 Round 3: 876 peptides, 103 chains. Longest chain 28 peptides. Score 0.525 Round 4: 878 peptides, 102 chains. Longest chain 31 peptides. Score 0.529 Round 5: 874 peptides, 104 chains. Longest chain 25 peptides. Score 0.521 Taking the results from Round 4 Chains 112, Residues 776, Estimated correctness of the model 0.0 % 13 chains (108 residues) have been docked in sequence ------------------------------------------------------ 18377 reflections ( 96.69 % complete ) and 27378 restraints for refining 12207 atoms. 24085 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2016 (Rfree = 0.000) for 12207 atoms. Found 49 (58 requested) and removed 115 (29 requested) atoms. Cycle 7: After refmac, R = 0.1942 (Rfree = 0.000) for 12002 atoms. Found 47 (57 requested) and removed 78 (28 requested) atoms. Cycle 8: After refmac, R = 0.1903 (Rfree = 0.000) for 11880 atoms. Found 48 (56 requested) and removed 71 (28 requested) atoms. Cycle 9: After refmac, R = 0.1869 (Rfree = 0.000) for 11805 atoms. Found 56 (56 requested) and removed 67 (28 requested) atoms. Cycle 10: After refmac, R = 0.1872 (Rfree = 0.000) for 11754 atoms. Found 55 (55 requested) and removed 51 (27 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.83 3.35 Search for helices and strands: 0 residues in 0 chains, 12237 seeds are put forward NCS extension: 36 residues added (1 deleted due to clashes), 12273 seeds are put forward Round 1: 777 peptides, 126 chains. Longest chain 14 peptides. Score 0.390 Round 2: 870 peptides, 108 chains. Longest chain 26 peptides. Score 0.507 Round 3: 886 peptides, 101 chains. Longest chain 34 peptides. Score 0.537 Round 4: 881 peptides, 107 chains. Longest chain 25 peptides. Score 0.517 Round 5: 880 peptides, 104 chains. Longest chain 27 peptides. Score 0.525 Taking the results from Round 3 Chains 103, Residues 785, Estimated correctness of the model 0.0 % 4 chains (30 residues) have been docked in sequence ------------------------------------------------------ 18377 reflections ( 96.69 % complete ) and 28195 restraints for refining 12351 atoms. 25057 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 11: After refmac, R = 0.1969 (Rfree = 0.000) for 12351 atoms. Found 55 (58 requested) and removed 136 (29 requested) atoms. Cycle 12: After refmac, R = 0.1928 (Rfree = 0.000) for 12135 atoms. Found 58 (58 requested) and removed 105 (29 requested) atoms. Cycle 13: After refmac, R = 0.1836 (Rfree = 0.000) for 12002 atoms. Found 57 (57 requested) and removed 68 (28 requested) atoms. Cycle 14: After refmac, R = 0.1863 (Rfree = 0.000) for 11925 atoms. Found 56 (56 requested) and removed 85 (28 requested) atoms. Failed to save intermediate PDB Cycle 15: After refmac, R = 0.1686 (Rfree = 0.000) for 11848 atoms. Found 56 (56 requested) and removed 61 (28 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.81 3.33 Search for helices and strands: 0 residues in 0 chains, 12270 seeds are put forward NCS extension: 16 residues added (1 deleted due to clashes), 12286 seeds are put forward Round 1: 737 peptides, 120 chains. Longest chain 15 peptides. Score 0.381 Round 2: 808 peptides, 110 chains. Longest chain 23 peptides. Score 0.462 Round 3: 796 peptides, 109 chains. Longest chain 27 peptides. Score 0.457 Round 4: 856 peptides, 119 chains. Longest chain 22 peptides. Score 0.466 Round 5: 871 peptides, 121 chains. Longest chain 22 peptides. Score 0.470 Taking the results from Round 5 Chains 125, Residues 750, Estimated correctness of the model 0.0 % 10 chains (64 residues) have been docked in sequence ------------------------------------------------------ 18377 reflections ( 96.69 % complete ) and 28189 restraints for refining 12396 atoms. 25135 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 16: After refmac, R = 0.1921 (Rfree = 0.000) for 12396 atoms. Found 53 (58 requested) and removed 92 (29 requested) atoms. Cycle 17: After refmac, R = 0.1862 (Rfree = 0.000) for 12252 atoms. Found 54 (58 requested) and removed 73 (29 requested) atoms. Cycle 18: After refmac, R = 0.1844 (Rfree = 0.000) for 12169 atoms. Found 58 (58 requested) and removed 66 (29 requested) atoms. Cycle 19: After refmac, R = 0.1764 (Rfree = 0.000) for 12096 atoms. Found 52 (57 requested) and removed 44 (28 requested) atoms. Cycle 20: After refmac, R = 0.1767 (Rfree = 0.000) for 12058 atoms. Found 57 (57 requested) and removed 50 (28 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.82 3.34 Search for helices and strands: 0 residues in 0 chains, 12518 seeds are put forward NCS extension: 20 residues added (0 deleted due to clashes), 12538 seeds are put forward Round 1: 728 peptides, 124 chains. Longest chain 20 peptides. Score 0.361 Round 2: 826 peptides, 121 chains. Longest chain 24 peptides. Score 0.440 Round 3: 836 peptides, 111 chains. Longest chain 22 peptides. Score 0.477 Round 4: 866 peptides, 112 chains. Longest chain 31 peptides. Score 0.493 Round 5: 881 peptides, 118 chains. Longest chain 23 peptides. Score 0.485 Taking the results from Round 4 Chains 118, Residues 754, Estimated correctness of the model 0.0 % 12 chains (100 residues) have been docked in sequence ------------------------------------------------------ 18377 reflections ( 96.69 % complete ) and 27747 restraints for refining 12394 atoms. 24528 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2008 (Rfree = 0.000) for 12394 atoms. Found 58 (58 requested) and removed 105 (29 requested) atoms. Cycle 22: After refmac, R = 0.1973 (Rfree = 0.000) for 12246 atoms. Found 58 (58 requested) and removed 77 (29 requested) atoms. Cycle 23: After refmac, R = 0.1881 (Rfree = 0.000) for 12172 atoms. Found 58 (58 requested) and removed 72 (29 requested) atoms. Cycle 24: After refmac, R = 0.1886 (Rfree = 0.000) for 12115 atoms. Found 57 (57 requested) and removed 57 (28 requested) atoms. Failed to save intermediate PDBFailed to save intermediate PDB Cycle 25: After refmac, R = 0.1857 (Rfree = 0.000) for 12070 atoms. Found 57 (57 requested) and removed 47 (28 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.84 3.36 Search for helices and strands: 0 residues in 0 chains, 12509 seeds are put forward NCS extension: 27 residues added (0 deleted due to clashes), 12536 seeds are put forward Round 1: 742 peptides, 131 chains. Longest chain 13 peptides. Score 0.349 Round 2: 807 peptides, 111 chains. Longest chain 27 peptides. Score 0.458 Round 3: 820 peptides, 119 chains. Longest chain 19 peptides. Score 0.442 Round 4: 817 peptides, 115 chains. Longest chain 23 peptides. Score 0.452 Round 5: 822 peptides, 112 chains. Longest chain 20 peptides. Score 0.465 Taking the results from Round 5 Chains 116, Residues 710, Estimated correctness of the model 0.0 % 8 chains (47 residues) have been docked in sequence ------------------------------------------------------ 18377 reflections ( 96.69 % complete ) and 28814 restraints for refining 12396 atoms. 25985 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 26: After refmac, R = 0.1902 (Rfree = 0.000) for 12396 atoms. Found 37 (58 requested) and removed 61 (29 requested) atoms. Cycle 27: After refmac, R = 0.1845 (Rfree = 0.000) for 12266 atoms. Found 58 (58 requested) and removed 57 (29 requested) atoms. Cycle 28: After refmac, R = 0.1865 (Rfree = 0.000) for 12221 atoms. Found 58 (58 requested) and removed 68 (29 requested) atoms. Cycle 29: After refmac, R = 0.1750 (Rfree = 0.000) for 12151 atoms. Found 57 (57 requested) and removed 48 (28 requested) atoms. Cycle 30: After refmac, R = 0.1822 (Rfree = 0.000) for 12122 atoms. Found 57 (57 requested) and removed 57 (28 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.80 3.32 Search for helices and strands: 0 residues in 0 chains, 12673 seeds are put forward NCS extension: 19 residues added (1 deleted due to clashes), 12692 seeds are put forward Round 1: 653 peptides, 132 chains. Longest chain 10 peptides. Score 0.275 Round 2: 769 peptides, 125 chains. Longest chain 17 peptides. Score 0.388 Round 3: 790 peptides, 118 chains. Longest chain 15 peptides. Score 0.425 Round 4: 801 peptides, 116 chains. Longest chain 19 peptides. Score 0.439 Round 5: 820 peptides, 116 chains. Longest chain 21 peptides. Score 0.451 Taking the results from Round 5 Chains 119, Residues 704, Estimated correctness of the model 0.0 % 8 chains (54 residues) have been docked in sequence ------------------------------------------------------ 18377 reflections ( 96.69 % complete ) and 28754 restraints for refining 12394 atoms. 25919 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1919 (Rfree = 0.000) for 12394 atoms. Found 58 (58 requested) and removed 96 (29 requested) atoms. Cycle 32: After refmac, R = 0.1817 (Rfree = 0.000) for 12278 atoms. Found 58 (58 requested) and removed 71 (29 requested) atoms. Cycle 33: After refmac, R = 0.1762 (Rfree = 0.000) for 12218 atoms. Found 58 (58 requested) and removed 69 (29 requested) atoms. Cycle 34: After refmac, R = 0.1407 (Rfree = 0.000) for 12154 atoms. Found 10 (57 requested) and removed 48 (28 requested) atoms. Cycle 35: After refmac, R = 0.1356 (Rfree = 0.000) for 12093 atoms. Found 16 (57 requested) and removed 40 (28 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.82 3.34 Search for helices and strands: 0 residues in 0 chains, 12467 seeds are put forward NCS extension: 33 residues added (2 deleted due to clashes), 12500 seeds are put forward Round 1: 633 peptides, 128 chains. Longest chain 9 peptides. Score 0.273 Round 2: 726 peptides, 117 chains. Longest chain 16 peptides. Score 0.382 Round 3: 750 peptides, 117 chains. Longest chain 17 peptides. Score 0.400 Round 4: 752 peptides, 115 chains. Longest chain 15 peptides. Score 0.408 Round 5: 743 peptides, 113 chains. Longest chain 18 peptides. Score 0.407 Taking the results from Round 4 Chains 115, Residues 637, Estimated correctness of the model 0.0 % 14 chains (82 residues) have been docked in sequence ------------------------------------------------------ 18377 reflections ( 96.69 % complete ) and 28717 restraints for refining 12397 atoms. 26088 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1843 (Rfree = 0.000) for 12397 atoms. Found 52 (58 requested) and removed 73 (29 requested) atoms. Failed to save intermediate PDB Cycle 37: After refmac, R = 0.1722 (Rfree = 0.000) for 12272 atoms. Found 54 (58 requested) and removed 52 (29 requested) atoms. Cycle 38: After refmac, R = 0.1778 (Rfree = 0.000) for 12229 atoms. Found 58 (58 requested) and removed 62 (29 requested) atoms. Cycle 39: After refmac, R = 0.1667 (Rfree = 0.000) for 12185 atoms. Found 52 (58 requested) and removed 51 (29 requested) atoms. Cycle 40: After refmac, R = 0.1349 (Rfree = 0.000) for 12157 atoms. Found 15 (57 requested) and removed 43 (28 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.80 3.32 Search for helices and strands: 0 residues in 0 chains, 12541 seeds are put forward NCS extension: 17 residues added (1 deleted due to clashes), 12558 seeds are put forward Round 1: 606 peptides, 125 chains. Longest chain 9 peptides. Score 0.261 Round 2: 717 peptides, 121 chains. Longest chain 16 peptides. Score 0.363 Round 3: 728 peptides, 114 chains. Longest chain 19 peptides. Score 0.394 Round 4: 737 peptides, 115 chains. Longest chain 15 peptides. Score 0.397 Round 5: 779 peptides, 117 chains. Longest chain 17 peptides. Score 0.420 Taking the results from Round 5 Chains 119, Residues 662, Estimated correctness of the model 0.0 % 9 chains (74 residues) have been docked in sequence ------------------------------------------------------ 18377 reflections ( 96.69 % complete ) and 28484 restraints for refining 12395 atoms. 25708 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1918 (Rfree = 0.000) for 12395 atoms. Found 57 (58 requested) and removed 70 (29 requested) atoms. Cycle 42: After refmac, R = 0.1815 (Rfree = 0.000) for 12298 atoms. Found 48 (58 requested) and removed 55 (29 requested) atoms. Cycle 43: After refmac, R = 0.1772 (Rfree = 0.000) for 12242 atoms. Found 54 (58 requested) and removed 55 (29 requested) atoms. Cycle 44: After refmac, R = 0.1793 (Rfree = 0.000) for 12190 atoms. Found 57 (58 requested) and removed 45 (29 requested) atoms. Cycle 45: After refmac, R = 0.1793 (Rfree = 0.000) for 12165 atoms. Found 57 (57 requested) and removed 45 (28 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.80 3.32 Search for helices and strands: 0 residues in 0 chains, 12558 seeds are put forward NCS extension: 23 residues added (3 deleted due to clashes), 12581 seeds are put forward Round 1: 591 peptides, 120 chains. Longest chain 17 peptides. Score 0.266 Round 2: 701 peptides, 119 chains. Longest chain 14 peptides. Score 0.357 Round 3: 714 peptides, 116 chains. Longest chain 19 peptides. Score 0.377 Round 4: 723 peptides, 111 chains. Longest chain 21 peptides. Score 0.400 Round 5: 690 peptides, 110 chains. Longest chain 22 peptides. Score 0.379 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 114, Residues 612, Estimated correctness of the model 0.0 % 8 chains (68 residues) have been docked in sequence Sequence coverage is 11 % Consider running further cycles of model building using 2p10-4_warpNtrace.pdb as input Building loops using Loopy2018 114 chains (612 residues) following loop building 8 chains (68 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 18377 reflections ( 96.69 % complete ) and 28768 restraints for refining 12394 atoms. 26244 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1902 (Rfree = 0.000) for 12394 atoms. Found 0 (58 requested) and removed 29 (29 requested) atoms. Cycle 47: After refmac, R = 0.1752 (Rfree = 0.000) for 12258 atoms. Found 0 (58 requested) and removed 29 (29 requested) atoms. Failed to save intermediate PDB Cycle 48: After refmac, R = 0.1749 (Rfree = 0.000) for 12180 atoms. Found 0 (58 requested) and removed 29 (29 requested) atoms. Cycle 49: After refmac, R = 0.1630 (Rfree = 0.000) for 12115 atoms. TimeTaking 140.77