Mon 24 Dec 07:36:19 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 2p10-3.6-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/2p10-3.6-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/2p10-3.6-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2p10-3.6-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/2p10-3.6-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2p10-3.6-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 07:36:23 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/2p10-3.6-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2p10-3.6-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 1517 and 0 Target number of residues in the AU: 1517 Target solvent content: 0.6462 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: 2p10-3.6-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: 2p10-3.6-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 3.600 Wilson plot Bfac: 75.71 25300 reflections ( 97.09 % complete ) and 0 restraints for refining 15229 atoms. Observations/parameters ratio is 0.42 ------------------------------------------------------ Starting model: R = 0.3068 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2640 (Rfree = 0.000) for 15229 atoms. Found 97 (97 requested) and removed 68 (48 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.48 3.04 Search for helices and strands: 0 residues in 0 chains, 15551 seeds are put forward NCS extension: 0 residues added, 15551 seeds are put forward Round 1: 875 peptides, 155 chains. Longest chain 18 peptides. Score 0.370 Round 2: 997 peptides, 124 chains. Longest chain 39 peptides. Score 0.539 Round 3: 1022 peptides, 125 chains. Longest chain 35 peptides. Score 0.551 Round 4: 1069 peptides, 121 chains. Longest chain 39 peptides. Score 0.588 Round 5: 1065 peptides, 116 chains. Longest chain 35 peptides. Score 0.598 Taking the results from Round 5 Chains 125, Residues 949, Estimated correctness of the model 13.9 % 20 chains (195 residues) have been docked in sequence ------------------------------------------------------ 25300 reflections ( 97.09 % complete ) and 26379 restraints for refining 12439 atoms. 22107 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2204 (Rfree = 0.000) for 12439 atoms. Found 79 (79 requested) and removed 102 (39 requested) atoms. Cycle 2: After refmac, R = 0.2083 (Rfree = 0.000) for 12209 atoms. Found 68 (79 requested) and removed 66 (39 requested) atoms. Failed to save intermediate PDB Cycle 3: After refmac, R = 0.1992 (Rfree = 0.000) for 12123 atoms. Found 49 (78 requested) and removed 57 (39 requested) atoms. Cycle 4: After refmac, R = 0.1929 (Rfree = 0.000) for 12057 atoms. Found 34 (77 requested) and removed 52 (38 requested) atoms. Cycle 5: After refmac, R = 0.1860 (Rfree = 0.000) for 11993 atoms. Found 28 (77 requested) and removed 53 (38 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.48 3.04 Search for helices and strands: 0 residues in 0 chains, 12429 seeds are put forward NCS extension: 13 residues added (8 deleted due to clashes), 12442 seeds are put forward Round 1: 963 peptides, 137 chains. Longest chain 25 peptides. Score 0.483 Round 2: 1053 peptides, 127 chains. Longest chain 32 peptides. Score 0.564 Round 3: 1010 peptides, 112 chains. Longest chain 24 peptides. Score 0.578 Round 4: 1038 peptides, 113 chains. Longest chain 31 peptides. Score 0.591 Round 5: 1016 peptides, 121 chains. Longest chain 27 peptides. Score 0.558 Taking the results from Round 4 Chains 132, Residues 925, Estimated correctness of the model 11.1 % 22 chains (257 residues) have been docked in sequence ------------------------------------------------------ 25300 reflections ( 97.09 % complete ) and 25713 restraints for refining 12443 atoms. 21291 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2219 (Rfree = 0.000) for 12443 atoms. Found 71 (79 requested) and removed 91 (39 requested) atoms. Cycle 7: After refmac, R = 0.2036 (Rfree = 0.000) for 12309 atoms. Found 34 (79 requested) and removed 64 (39 requested) atoms. Cycle 8: After refmac, R = 0.1959 (Rfree = 0.000) for 12220 atoms. Found 25 (78 requested) and removed 57 (39 requested) atoms. Cycle 9: After refmac, R = 0.1895 (Rfree = 0.000) for 12151 atoms. Found 28 (78 requested) and removed 52 (39 requested) atoms. Cycle 10: After refmac, R = 0.1839 (Rfree = 0.000) for 12107 atoms. Found 20 (77 requested) and removed 45 (38 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.46 3.02 Search for helices and strands: 0 residues in 0 chains, 12571 seeds are put forward NCS extension: 20 residues added (8 deleted due to clashes), 12591 seeds are put forward Round 1: 956 peptides, 133 chains. Longest chain 30 peptides. Score 0.490 Round 2: 1026 peptides, 119 chains. Longest chain 32 peptides. Score 0.569 Round 3: 1014 peptides, 116 chains. Longest chain 27 peptides. Score 0.570 Round 4: 1028 peptides, 121 chains. Longest chain 22 peptides. Score 0.565 Round 5: 1034 peptides, 115 chains. Longest chain 32 peptides. Score 0.584 Taking the results from Round 5 Chains 118, Residues 919, Estimated correctness of the model 8.3 % 16 chains (168 residues) have been docked in sequence ------------------------------------------------------ 25300 reflections ( 97.09 % complete ) and 26664 restraints for refining 12443 atoms. 22575 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2101 (Rfree = 0.000) for 12443 atoms. Found 73 (79 requested) and removed 80 (39 requested) atoms. Cycle 12: After refmac, R = 0.1882 (Rfree = 0.000) for 12336 atoms. Found 28 (79 requested) and removed 64 (39 requested) atoms. Cycle 13: After refmac, R = 0.1812 (Rfree = 0.000) for 12242 atoms. Found 28 (78 requested) and removed 58 (39 requested) atoms. Cycle 14: After refmac, R = 0.1745 (Rfree = 0.000) for 12188 atoms. Found 39 (78 requested) and removed 64 (39 requested) atoms. Failed to save intermediate PDB Cycle 15: After refmac, R = 0.1695 (Rfree = 0.000) for 12146 atoms. Found 16 (78 requested) and removed 45 (39 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.44 3.01 Search for helices and strands: 0 residues in 0 chains, 12562 seeds are put forward NCS extension: 11 residues added (12 deleted due to clashes), 12573 seeds are put forward Round 1: 916 peptides, 131 chains. Longest chain 28 peptides. Score 0.470 Round 2: 994 peptides, 121 chains. Longest chain 26 peptides. Score 0.546 Round 3: 990 peptides, 121 chains. Longest chain 26 peptides. Score 0.543 Round 4: 991 peptides, 120 chains. Longest chain 31 peptides. Score 0.547 Round 5: 1007 peptides, 125 chains. Longest chain 25 peptides. Score 0.543 Taking the results from Round 4 Chains 130, Residues 871, Estimated correctness of the model 0.0 % 15 chains (165 residues) have been docked in sequence ------------------------------------------------------ 25300 reflections ( 97.09 % complete ) and 26831 restraints for refining 12443 atoms. 22927 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2021 (Rfree = 0.000) for 12443 atoms. Found 51 (79 requested) and removed 80 (39 requested) atoms. Cycle 17: After refmac, R = 0.1858 (Rfree = 0.000) for 12345 atoms. Found 26 (79 requested) and removed 55 (39 requested) atoms. Cycle 18: After refmac, R = 0.1802 (Rfree = 0.000) for 12299 atoms. Found 21 (79 requested) and removed 54 (39 requested) atoms. Failed to save intermediate PDB Cycle 19: After refmac, R = 0.1754 (Rfree = 0.000) for 12252 atoms. Found 24 (78 requested) and removed 47 (39 requested) atoms. Cycle 20: After refmac, R = 0.1715 (Rfree = 0.000) for 12212 atoms. Found 25 (78 requested) and removed 41 (39 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.44 3.01 Search for helices and strands: 0 residues in 0 chains, 12650 seeds are put forward NCS extension: 18 residues added (9 deleted due to clashes), 12668 seeds are put forward Round 1: 914 peptides, 141 chains. Longest chain 20 peptides. Score 0.440 Round 2: 970 peptides, 118 chains. Longest chain 33 peptides. Score 0.540 Round 3: 967 peptides, 117 chains. Longest chain 34 peptides. Score 0.541 Round 4: 991 peptides, 121 chains. Longest chain 24 peptides. Score 0.544 Round 5: 985 peptides, 121 chains. Longest chain 25 peptides. Score 0.540 Taking the results from Round 4 Chains 131, Residues 870, Estimated correctness of the model 0.0 % 19 chains (153 residues) have been docked in sequence ------------------------------------------------------ 25300 reflections ( 97.09 % complete ) and 27186 restraints for refining 12445 atoms. 23396 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2068 (Rfree = 0.000) for 12445 atoms. Found 69 (79 requested) and removed 81 (39 requested) atoms. Cycle 22: After refmac, R = 0.1917 (Rfree = 0.000) for 12382 atoms. Found 32 (79 requested) and removed 58 (39 requested) atoms. Cycle 23: After refmac, R = 0.1849 (Rfree = 0.000) for 12326 atoms. Found 29 (79 requested) and removed 58 (39 requested) atoms. Cycle 24: After refmac, R = 0.1789 (Rfree = 0.000) for 12272 atoms. Found 26 (78 requested) and removed 45 (39 requested) atoms. Cycle 25: After refmac, R = 0.1751 (Rfree = 0.000) for 12233 atoms. Found 18 (78 requested) and removed 45 (39 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.46 3.02 Search for helices and strands: 0 residues in 0 chains, 12584 seeds are put forward NCS extension: 30 residues added (4 deleted due to clashes), 12614 seeds are put forward Round 1: 891 peptides, 150 chains. Longest chain 16 peptides. Score 0.397 Round 2: 980 peptides, 135 chains. Longest chain 21 peptides. Score 0.499 Round 3: 967 peptides, 128 chains. Longest chain 26 peptides. Score 0.511 Round 4: 995 peptides, 130 chains. Longest chain 24 peptides. Score 0.522 Round 5: 989 peptides, 131 chains. Longest chain 24 peptides. Score 0.516 Taking the results from Round 4 Chains 137, Residues 865, Estimated correctness of the model 0.0 % 19 chains (159 residues) have been docked in sequence ------------------------------------------------------ 25300 reflections ( 97.09 % complete ) and 26882 restraints for refining 12443 atoms. 23030 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2037 (Rfree = 0.000) for 12443 atoms. Found 64 (79 requested) and removed 68 (39 requested) atoms. Cycle 27: After refmac, R = 0.1868 (Rfree = 0.000) for 12393 atoms. Found 20 (79 requested) and removed 60 (39 requested) atoms. Failed to save intermediate PDB Cycle 28: After refmac, R = 0.1839 (Rfree = 0.000) for 12327 atoms. Found 30 (79 requested) and removed 52 (39 requested) atoms. Cycle 29: After refmac, R = 0.1786 (Rfree = 0.000) for 12287 atoms. Found 26 (78 requested) and removed 45 (39 requested) atoms. Cycle 30: After refmac, R = 0.1719 (Rfree = 0.000) for 12254 atoms. Found 13 (78 requested) and removed 41 (39 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.47 3.03 Search for helices and strands: 0 residues in 0 chains, 12649 seeds are put forward NCS extension: 21 residues added (3 deleted due to clashes), 12670 seeds are put forward Round 1: 846 peptides, 139 chains. Longest chain 27 peptides. Score 0.399 Round 2: 892 peptides, 128 chains. Longest chain 23 peptides. Score 0.463 Round 3: 918 peptides, 125 chains. Longest chain 28 peptides. Score 0.489 Round 4: 899 peptides, 119 chains. Longest chain 25 peptides. Score 0.494 Round 5: 900 peptides, 116 chains. Longest chain 26 peptides. Score 0.503 Taking the results from Round 5 Chains 120, Residues 784, Estimated correctness of the model 0.0 % 8 chains (59 residues) have been docked in sequence ------------------------------------------------------ 25300 reflections ( 97.09 % complete ) and 28618 restraints for refining 12445 atoms. 25438 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1944 (Rfree = 0.000) for 12445 atoms. Found 57 (79 requested) and removed 63 (39 requested) atoms. Cycle 32: After refmac, R = 0.1801 (Rfree = 0.000) for 12387 atoms. Found 21 (79 requested) and removed 45 (39 requested) atoms. Cycle 33: After refmac, R = 0.1743 (Rfree = 0.000) for 12338 atoms. Found 25 (79 requested) and removed 50 (39 requested) atoms. Cycle 34: After refmac, R = 0.1697 (Rfree = 0.000) for 12292 atoms. Found 32 (78 requested) and removed 48 (39 requested) atoms. Cycle 35: After refmac, R = 0.1656 (Rfree = 0.000) for 12262 atoms. Found 35 (78 requested) and removed 45 (39 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.47 3.03 Search for helices and strands: 0 residues in 0 chains, 12659 seeds are put forward NCS extension: 15 residues added (1 deleted due to clashes), 12674 seeds are put forward Round 1: 788 peptides, 136 chains. Longest chain 27 peptides. Score 0.367 Round 2: 901 peptides, 127 chains. Longest chain 43 peptides. Score 0.472 Round 3: 915 peptides, 120 chains. Longest chain 25 peptides. Score 0.501 Round 4: 893 peptides, 122 chains. Longest chain 22 peptides. Score 0.481 Round 5: 893 peptides, 123 chains. Longest chain 23 peptides. Score 0.478 Taking the results from Round 3 Chains 127, Residues 795, Estimated correctness of the model 0.0 % 19 chains (155 residues) have been docked in sequence ------------------------------------------------------ 25300 reflections ( 97.09 % complete ) and 27389 restraints for refining 12445 atoms. 23881 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1935 (Rfree = 0.000) for 12445 atoms. Found 62 (79 requested) and removed 67 (39 requested) atoms. Cycle 37: After refmac, R = 0.1802 (Rfree = 0.000) for 12398 atoms. Found 22 (79 requested) and removed 50 (39 requested) atoms. Cycle 38: After refmac, R = 0.1806 (Rfree = 0.000) for 12343 atoms. Found 40 (79 requested) and removed 51 (39 requested) atoms. Cycle 39: After refmac, R = 0.1766 (Rfree = 0.000) for 12319 atoms. Found 56 (79 requested) and removed 56 (39 requested) atoms. Cycle 40: After refmac, R = 0.1729 (Rfree = 0.000) for 12300 atoms. Found 45 (79 requested) and removed 52 (39 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.45 3.01 Search for helices and strands: 0 residues in 0 chains, 12737 seeds are put forward NCS extension: 15 residues added (0 deleted due to clashes), 12752 seeds are put forward Round 1: 812 peptides, 137 chains. Longest chain 18 peptides. Score 0.381 Round 2: 861 peptides, 120 chains. Longest chain 31 peptides. Score 0.467 Round 3: 888 peptides, 124 chains. Longest chain 26 peptides. Score 0.472 Round 4: 879 peptides, 125 chains. Longest chain 22 peptides. Score 0.464 Round 5: 880 peptides, 123 chains. Longest chain 19 peptides. Score 0.470 Taking the results from Round 3 Chains 127, Residues 764, Estimated correctness of the model 0.0 % 10 chains (99 residues) have been docked in sequence ------------------------------------------------------ 25300 reflections ( 97.09 % complete ) and 27754 restraints for refining 12442 atoms. 24497 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1933 (Rfree = 0.000) for 12442 atoms. Found 67 (79 requested) and removed 59 (39 requested) atoms. Cycle 42: After refmac, R = 0.1813 (Rfree = 0.000) for 12399 atoms. Found 31 (79 requested) and removed 50 (39 requested) atoms. Cycle 43: After refmac, R = 0.1788 (Rfree = 0.000) for 12357 atoms. Found 53 (79 requested) and removed 52 (39 requested) atoms. Cycle 44: After refmac, R = 0.1739 (Rfree = 0.000) for 12339 atoms. Found 35 (79 requested) and removed 44 (39 requested) atoms. Cycle 45: After refmac, R = 0.1711 (Rfree = 0.000) for 12317 atoms. Found 39 (79 requested) and removed 48 (39 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.47 3.03 Search for helices and strands: 0 residues in 0 chains, 12819 seeds are put forward NCS extension: 16 residues added (3 deleted due to clashes), 12835 seeds are put forward Round 1: 746 peptides, 124 chains. Longest chain 20 peptides. Score 0.374 Round 2: 873 peptides, 126 chains. Longest chain 26 peptides. Score 0.457 Round 3: 855 peptides, 121 chains. Longest chain 24 peptides. Score 0.460 Round 4: 833 peptides, 118 chains. Longest chain 20 peptides. Score 0.454 Round 5: 828 peptides, 122 chains. Longest chain 24 peptides. Score 0.439 Taking the results from Round 3 Last building cycle: Chain fragments will be rearranged Chains 126, Residues 734, Estimated correctness of the model 0.0 % 8 chains (95 residues) have been docked in sequence Sequence coverage is 12 % Consider running further cycles of model building using 2p10-3_warpNtrace.pdb as input Building loops using Loopy2018 126 chains (734 residues) following loop building 8 chains (95 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 25300 reflections ( 97.09 % complete ) and 28287 restraints for refining 12442 atoms. 25149 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1890 (Rfree = 0.000) for 12442 atoms. Found 0 (79 requested) and removed 39 (39 requested) atoms. Cycle 47: After refmac, R = 0.1813 (Rfree = 0.000) for 12352 atoms. Found 0 (79 requested) and removed 39 (39 requested) atoms. Cycle 48: After refmac, R = 0.1815 (Rfree = 0.000) for 12285 atoms. Found 0 (78 requested) and removed 29 (39 requested) atoms. Cycle 49: After refmac, R = 0.1803 (Rfree = 0.000) for 12235 atoms. TimeTaking 143.85