Sun 23 Dec 22:22:52 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 1vkn-3.2-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/1vkn-3.2-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/1vkn-3.2-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vkn-3.2-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/1vkn-3.2-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vkn-3.2-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 22:23:02 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/1vkn-3.2-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vkn-3.2-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 1034 and 0 Target number of residues in the AU: 1034 Target solvent content: 0.6187 Checking the provided sequence file Detected sequence length: 351 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 4 Adjusted target number of residues: 1404 Adjusted target solvent content: 0.48 Input MTZ file: 1vkn-3.2-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: 4 Cell parameters: 85.135 92.128 101.299 90.000 112.538 90.000 Input sequence file: 1vkn-3.2-parrot-hancs.fasta_lf Building free atoms model in initial map for 11232 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: 93.562 3.200 Wilson plot Bfac: 60.76 23822 reflections ( 98.91 % complete ) and 0 restraints for refining 12508 atoms. Observations/parameters ratio is 0.48 ------------------------------------------------------ Starting model: R = 0.2970 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2265 (Rfree = 0.000) for 12508 atoms. Found 112 (112 requested) and removed 95 (56 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.15 3.24 Search for helices and strands: 0 residues in 0 chains, 12781 seeds are put forward NCS extension: 0 residues added, 12781 seeds are put forward Round 1: 740 peptides, 122 chains. Longest chain 18 peptides. Score 0.459 Round 2: 879 peptides, 112 chains. Longest chain 27 peptides. Score 0.621 Round 3: 925 peptides, 106 chains. Longest chain 34 peptides. Score 0.674 Round 4: 983 peptides, 100 chains. Longest chain 30 peptides. Score 0.728 Round 5: 999 peptides, 94 chains. Longest chain 33 peptides. Score 0.752 Taking the results from Round 5 Chains 103, Residues 905, Estimated correctness of the model 75.4 % 19 chains (245 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 283 B and 288 B 102 chains (906 residues) following loop building 18 chains (249 residues) in sequence following loop building ------------------------------------------------------ 23822 reflections ( 98.91 % complete ) and 19148 restraints for refining 10249 atoms. 14762 conditional restraints added. Observations/parameters ratio is 0.58 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2338 (Rfree = 0.000) for 10249 atoms. Found 92 (92 requested) and removed 112 (46 requested) atoms. Cycle 2: After refmac, R = 0.2153 (Rfree = 0.000) for 10102 atoms. Found 59 (89 requested) and removed 58 (45 requested) atoms. Cycle 3: After refmac, R = 0.2072 (Rfree = 0.000) for 10042 atoms. Found 39 (86 requested) and removed 48 (45 requested) atoms. Cycle 4: After refmac, R = 0.2003 (Rfree = 0.000) for 10008 atoms. Found 26 (85 requested) and removed 47 (45 requested) atoms. Cycle 5: After refmac, R = 0.1968 (Rfree = 0.000) for 9965 atoms. Found 25 (82 requested) and removed 45 (44 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.16 3.25 Search for helices and strands: 0 residues in 0 chains, 10310 seeds are put forward NCS extension: 30 residues added (35 deleted due to clashes), 10340 seeds are put forward Round 1: 903 peptides, 109 chains. Longest chain 33 peptides. Score 0.649 Round 2: 950 peptides, 86 chains. Longest chain 31 peptides. Score 0.747 Round 3: 962 peptides, 90 chains. Longest chain 38 peptides. Score 0.743 Round 4: 948 peptides, 90 chains. Longest chain 43 peptides. Score 0.735 Round 5: 963 peptides, 87 chains. Longest chain 51 peptides. Score 0.751 Taking the results from Round 5 Chains 97, Residues 876, Estimated correctness of the model 75.2 % 17 chains (300 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 230 B and 233 B 95 chains (873 residues) following loop building 16 chains (302 residues) in sequence following loop building ------------------------------------------------------ 23822 reflections ( 98.91 % complete ) and 19153 restraints for refining 10254 atoms. 14587 conditional restraints added. Observations/parameters ratio is 0.58 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2385 (Rfree = 0.000) for 10254 atoms. Found 83 (83 requested) and removed 95 (46 requested) atoms. Cycle 7: After refmac, R = 0.2138 (Rfree = 0.000) for 10184 atoms. Found 42 (80 requested) and removed 59 (45 requested) atoms. Cycle 8: After refmac, R = 0.2045 (Rfree = 0.000) for 10134 atoms. Found 35 (78 requested) and removed 54 (45 requested) atoms. Failed to save intermediate PDB Cycle 9: After refmac, R = 0.1962 (Rfree = 0.000) for 10095 atoms. Found 20 (76 requested) and removed 49 (45 requested) atoms. Cycle 10: After refmac, R = 0.1912 (Rfree = 0.000) for 10048 atoms. Found 23 (74 requested) and removed 45 (45 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.15 3.24 Search for helices and strands: 0 residues in 0 chains, 10374 seeds are put forward NCS extension: 20 residues added (29 deleted due to clashes), 10394 seeds are put forward Round 1: 854 peptides, 104 chains. Longest chain 29 peptides. Score 0.630 Round 2: 943 peptides, 96 chains. Longest chain 39 peptides. Score 0.715 Round 3: 958 peptides, 93 chains. Longest chain 59 peptides. Score 0.732 Round 4: 943 peptides, 99 chains. Longest chain 31 peptides. Score 0.707 Round 5: 961 peptides, 96 chains. Longest chain 35 peptides. Score 0.726 Taking the results from Round 3 Chains 103, Residues 865, Estimated correctness of the model 71.7 % 19 chains (349 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 58 B and 69 B Built loop between residues 291 B and 296 B 100 chains (872 residues) following loop building 17 chains (363 residues) in sequence following loop building ------------------------------------------------------ 23822 reflections ( 98.91 % complete ) and 18665 restraints for refining 10251 atoms. 13802 conditional restraints added. Observations/parameters ratio is 0.58 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2346 (Rfree = 0.000) for 10251 atoms. Found 74 (74 requested) and removed 90 (46 requested) atoms. Cycle 12: After refmac, R = 0.2171 (Rfree = 0.000) for 10161 atoms. Found 52 (71 requested) and removed 52 (45 requested) atoms. Cycle 13: After refmac, R = 0.2109 (Rfree = 0.000) for 10117 atoms. Found 35 (69 requested) and removed 45 (45 requested) atoms. Cycle 14: After refmac, R = 0.2090 (Rfree = 0.000) for 10094 atoms. Found 25 (67 requested) and removed 46 (45 requested) atoms. Cycle 15: After refmac, R = 0.2076 (Rfree = 0.000) for 10056 atoms. Found 29 (65 requested) and removed 45 (45 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.16 3.25 Search for helices and strands: 0 residues in 0 chains, 10383 seeds are put forward NCS extension: 21 residues added (19 deleted due to clashes), 10404 seeds are put forward Round 1: 863 peptides, 109 chains. Longest chain 35 peptides. Score 0.619 Round 2: 906 peptides, 95 chains. Longest chain 34 peptides. Score 0.695 Round 3: 919 peptides, 97 chains. Longest chain 38 peptides. Score 0.697 Round 4: 876 peptides, 101 chains. Longest chain 35 peptides. Score 0.656 Round 5: 904 peptides, 98 chains. Longest chain 33 peptides. Score 0.685 Taking the results from Round 3 Chains 104, Residues 822, Estimated correctness of the model 64.5 % 14 chains (205 residues) have been docked in sequence ------------------------------------------------------ 23822 reflections ( 98.91 % complete ) and 20636 restraints for refining 10253 atoms. 16582 conditional restraints added. Observations/parameters ratio is 0.58 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2240 (Rfree = 0.000) for 10253 atoms. Found 64 (64 requested) and removed 76 (46 requested) atoms. Cycle 17: After refmac, R = 0.2097 (Rfree = 0.000) for 10209 atoms. Found 41 (64 requested) and removed 49 (45 requested) atoms. Cycle 18: After refmac, R = 0.2058 (Rfree = 0.000) for 10183 atoms. Found 33 (64 requested) and removed 46 (45 requested) atoms. Cycle 19: After refmac, R = 0.1972 (Rfree = 0.000) for 10153 atoms. Found 21 (64 requested) and removed 46 (45 requested) atoms. Cycle 20: After refmac, R = 0.1920 (Rfree = 0.000) for 10108 atoms. Found 27 (63 requested) and removed 45 (45 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.16 3.25 Search for helices and strands: 0 residues in 0 chains, 10367 seeds are put forward NCS extension: 20 residues added (4 deleted due to clashes), 10387 seeds are put forward Round 1: 797 peptides, 112 chains. Longest chain 18 peptides. Score 0.554 Round 2: 875 peptides, 99 chains. Longest chain 31 peptides. Score 0.662 Round 3: 850 peptides, 94 chains. Longest chain 40 peptides. Score 0.660 Round 4: 856 peptides, 100 chains. Longest chain 42 peptides. Score 0.645 Round 5: 880 peptides, 94 chains. Longest chain 40 peptides. Score 0.681 Taking the results from Round 5 Chains 97, Residues 786, Estimated correctness of the model 61.0 % 5 chains (99 residues) have been docked in sequence ------------------------------------------------------ 23822 reflections ( 98.91 % complete ) and 21939 restraints for refining 10253 atoms. 18529 conditional restraints added. Observations/parameters ratio is 0.58 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2170 (Rfree = 0.000) for 10253 atoms. Found 64 (64 requested) and removed 63 (46 requested) atoms. Cycle 22: After refmac, R = 0.1990 (Rfree = 0.000) for 10223 atoms. Found 31 (64 requested) and removed 50 (46 requested) atoms. Cycle 23: After refmac, R = 0.1957 (Rfree = 0.000) for 10181 atoms. Found 28 (64 requested) and removed 48 (45 requested) atoms. Cycle 24: After refmac, R = 0.1912 (Rfree = 0.000) for 10146 atoms. Found 30 (64 requested) and removed 47 (45 requested) atoms. Cycle 25: After refmac, R = 0.1866 (Rfree = 0.000) for 10116 atoms. Found 31 (63 requested) and removed 45 (45 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.17 3.26 Search for helices and strands: 0 residues in 0 chains, 10430 seeds are put forward NCS extension: 15 residues added (8 deleted due to clashes), 10445 seeds are put forward Round 1: 738 peptides, 105 chains. Longest chain 23 peptides. Score 0.528 Round 2: 861 peptides, 95 chains. Longest chain 24 peptides. Score 0.665 Round 3: 870 peptides, 96 chains. Longest chain 31 peptides. Score 0.668 Round 4: 845 peptides, 89 chains. Longest chain 27 peptides. Score 0.673 Round 5: 846 peptides, 84 chains. Longest chain 35 peptides. Score 0.689 Taking the results from Round 5 Chains 91, Residues 762, Estimated correctness of the model 62.8 % 10 chains (159 residues) have been docked in sequence ------------------------------------------------------ 23822 reflections ( 98.91 % complete ) and 21409 restraints for refining 10254 atoms. 17834 conditional restraints added. Observations/parameters ratio is 0.58 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2136 (Rfree = 0.000) for 10254 atoms. Found 64 (64 requested) and removed 65 (46 requested) atoms. Cycle 27: After refmac, R = 0.1976 (Rfree = 0.000) for 10226 atoms. Found 39 (64 requested) and removed 49 (46 requested) atoms. Cycle 28: After refmac, R = 0.1958 (Rfree = 0.000) for 10195 atoms. Found 48 (64 requested) and removed 46 (45 requested) atoms. Cycle 29: After refmac, R = 0.1908 (Rfree = 0.000) for 10186 atoms. Found 23 (64 requested) and removed 45 (45 requested) atoms. Cycle 30: After refmac, R = 0.1841 (Rfree = 0.000) for 10153 atoms. Found 27 (64 requested) and removed 45 (45 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.17 3.26 Search for helices and strands: 0 residues in 0 chains, 10433 seeds are put forward NCS extension: 18 residues added (10 deleted due to clashes), 10451 seeds are put forward Round 1: 768 peptides, 105 chains. Longest chain 29 peptides. Score 0.555 Round 2: 855 peptides, 100 chains. Longest chain 33 peptides. Score 0.644 Round 3: 846 peptides, 99 chains. Longest chain 27 peptides. Score 0.641 Round 4: 856 peptides, 101 chains. Longest chain 27 peptides. Score 0.641 Round 5: 841 peptides, 100 chains. Longest chain 27 peptides. Score 0.633 Taking the results from Round 2 Chains 107, Residues 755, Estimated correctness of the model 52.4 % 11 chains (174 residues) have been docked in sequence ------------------------------------------------------ 23822 reflections ( 98.91 % complete ) and 21135 restraints for refining 10254 atoms. 17515 conditional restraints added. Observations/parameters ratio is 0.58 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2028 (Rfree = 0.000) for 10254 atoms. Found 64 (64 requested) and removed 64 (46 requested) atoms. Cycle 32: After refmac, R = 0.1911 (Rfree = 0.000) for 10229 atoms. Found 40 (64 requested) and removed 50 (46 requested) atoms. Cycle 33: After refmac, R = 0.1890 (Rfree = 0.000) for 10196 atoms. Found 33 (64 requested) and removed 46 (45 requested) atoms. Cycle 34: After refmac, R = 0.1835 (Rfree = 0.000) for 10171 atoms. Found 24 (64 requested) and removed 45 (45 requested) atoms. Cycle 35: After refmac, R = 0.1815 (Rfree = 0.000) for 10144 atoms. Found 21 (64 requested) and removed 46 (45 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.16 3.25 Search for helices and strands: 0 residues in 0 chains, 10421 seeds are put forward NCS extension: 13 residues added (13 deleted due to clashes), 10434 seeds are put forward Round 1: 733 peptides, 106 chains. Longest chain 17 peptides. Score 0.520 Round 2: 792 peptides, 94 chains. Longest chain 26 peptides. Score 0.617 Round 3: 802 peptides, 94 chains. Longest chain 27 peptides. Score 0.625 Round 4: 821 peptides, 95 chains. Longest chain 28 peptides. Score 0.636 Round 5: 792 peptides, 96 chains. Longest chain 25 peptides. Score 0.610 Taking the results from Round 4 Chains 96, Residues 726, Estimated correctness of the model 50.4 % 8 chains (98 residues) have been docked in sequence ------------------------------------------------------ 23822 reflections ( 98.91 % complete ) and 22239 restraints for refining 10253 atoms. 19047 conditional restraints added. Observations/parameters ratio is 0.58 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2046 (Rfree = 0.000) for 10253 atoms. Found 64 (64 requested) and removed 63 (46 requested) atoms. Cycle 37: After refmac, R = 0.1924 (Rfree = 0.000) for 10223 atoms. Found 28 (64 requested) and removed 52 (46 requested) atoms. Cycle 38: After refmac, R = 0.1913 (Rfree = 0.000) for 10187 atoms. Found 36 (64 requested) and removed 45 (45 requested) atoms. Cycle 39: After refmac, R = 0.1862 (Rfree = 0.000) for 10164 atoms. Found 33 (64 requested) and removed 45 (45 requested) atoms. Cycle 40: After refmac, R = 0.1803 (Rfree = 0.000) for 10142 atoms. Found 20 (64 requested) and removed 45 (45 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.16 3.25 Search for helices and strands: 0 residues in 0 chains, 10395 seeds are put forward NCS extension: 28 residues added (9 deleted due to clashes), 10423 seeds are put forward Round 1: 685 peptides, 100 chains. Longest chain 18 peptides. Score 0.499 Round 2: 751 peptides, 90 chains. Longest chain 29 peptides. Score 0.598 Round 3: 777 peptides, 96 chains. Longest chain 39 peptides. Score 0.597 Round 4: 768 peptides, 89 chains. Longest chain 25 peptides. Score 0.616 Round 5: 763 peptides, 92 chains. Longest chain 26 peptides. Score 0.601 Taking the results from Round 4 Chains 91, Residues 679, Estimated correctness of the model 45.3 % 10 chains (103 residues) have been docked in sequence ------------------------------------------------------ 23822 reflections ( 98.91 % complete ) and 22384 restraints for refining 10253 atoms. 19351 conditional restraints added. Observations/parameters ratio is 0.58 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2025 (Rfree = 0.000) for 10253 atoms. Found 63 (64 requested) and removed 56 (46 requested) atoms. Cycle 42: After refmac, R = 0.1923 (Rfree = 0.000) for 10240 atoms. Found 49 (64 requested) and removed 50 (46 requested) atoms. Cycle 43: After refmac, R = 0.1902 (Rfree = 0.000) for 10231 atoms. Found 37 (64 requested) and removed 45 (45 requested) atoms. Cycle 44: After refmac, R = 0.1839 (Rfree = 0.000) for 10207 atoms. Found 29 (64 requested) and removed 45 (45 requested) atoms. Cycle 45: After refmac, R = 0.1820 (Rfree = 0.000) for 10188 atoms. Found 21 (64 requested) and removed 45 (45 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.17 3.26 Search for helices and strands: 0 residues in 0 chains, 10421 seeds are put forward NCS extension: 18 residues added (11 deleted due to clashes), 10439 seeds are put forward Round 1: 661 peptides, 105 chains. Longest chain 18 peptides. Score 0.454 Round 2: 731 peptides, 95 chains. Longest chain 30 peptides. Score 0.562 Round 3: 738 peptides, 99 chains. Longest chain 26 peptides. Score 0.553 Round 4: 764 peptides, 97 chains. Longest chain 29 peptides. Score 0.583 Round 5: 736 peptides, 93 chains. Longest chain 25 peptides. Score 0.574 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 100, Residues 667, Estimated correctness of the model 36.4 % 7 chains (52 residues) have been docked in sequence Sequence coverage is 7 % Consider running further cycles of model building using 1vkn-3_warpNtrace.pdb as input Building loops using Loopy2018 100 chains (667 residues) following loop building 7 chains (52 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 23822 reflections ( 98.91 % complete ) and 22936 restraints for refining 10253 atoms. 20165 conditional restraints added. Observations/parameters ratio is 0.58 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1997 (Rfree = 0.000) for 10253 atoms. Found 0 (64 requested) and removed 42 (46 requested) atoms. Cycle 47: After refmac, R = 0.1976 (Rfree = 0.000) for 10205 atoms. Found 0 (64 requested) and removed 24 (45 requested) atoms. Cycle 48: After refmac, R = 0.1930 (Rfree = 0.000) for 10170 atoms. Found 0 (64 requested) and removed 14 (45 requested) atoms. Cycle 49: After refmac, R = 0.1896 (Rfree = 0.000) for 10151 atoms. TimeTaking 122.37