Tue 25 Dec 19:27:55 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 2obn-3.2-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2obn-3.2-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2obn-3.2-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2obn-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/2obn-3.2-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2obn-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 ============================================================ Tue 25 Dec 19:28:05 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/2obn-3.2-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2obn-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 948 and 0 Target number of residues in the AU: 948 Target solvent content: 0.6204 Checking the provided sequence file Detected sequence length: 349 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 4 Adjusted target number of residues: 1396 Adjusted target solvent content: 0.44 Input MTZ file: 2obn-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: 75.040 122.990 75.170 90.000 103.099 90.000 Input sequence file: 2obn-3.2-parrot-hancs.fasta_lf Building free atoms model in initial map for 11168 target number of atoms Had to go as low as 0.60 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: 73.214 3.200 Wilson plot Bfac: 61.60 21957 reflections ( 99.70 % complete ) and 0 restraints for refining 12377 atoms. Observations/parameters ratio is 0.44 ------------------------------------------------------ Starting model: R = 0.2922 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2192 (Rfree = 0.000) for 12377 atoms. Found 65 (111 requested) and removed 88 (55 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.16 3.42 Search for helices and strands: 0 residues in 0 chains, 12624 seeds are put forward NCS extension: 0 residues added, 12624 seeds are put forward Round 1: 715 peptides, 125 chains. Longest chain 18 peptides. Score 0.436 Round 2: 872 peptides, 115 chains. Longest chain 23 peptides. Score 0.629 Round 3: 880 peptides, 107 chains. Longest chain 27 peptides. Score 0.663 Round 4: 925 peptides, 103 chains. Longest chain 40 peptides. Score 0.708 Round 5: 954 peptides, 107 chains. Longest chain 33 peptides. Score 0.715 Taking the results from Round 5 Chains 124, Residues 847, Estimated correctness of the model 68.3 % 21 chains (228 residues) have been docked in sequence Building loops using Loopy2018 124 chains (847 residues) following loop building 21 chains (228 residues) in sequence following loop building ------------------------------------------------------ 21957 reflections ( 99.70 % complete ) and 19860 restraints for refining 10190 atoms. 15882 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2347 (Rfree = 0.000) for 10190 atoms. Found 68 (91 requested) and removed 80 (45 requested) atoms. Failed to save intermediate PDB Cycle 2: After refmac, R = 0.2154 (Rfree = 0.000) for 10048 atoms. Found 28 (89 requested) and removed 60 (45 requested) atoms. Cycle 3: After refmac, R = 0.2073 (Rfree = 0.000) for 9970 atoms. Found 23 (85 requested) and removed 56 (44 requested) atoms. Cycle 4: After refmac, R = 0.2009 (Rfree = 0.000) for 9906 atoms. Found 18 (84 requested) and removed 46 (44 requested) atoms. Failed to save intermediate PDB Cycle 5: After refmac, R = 0.1969 (Rfree = 0.000) for 9863 atoms. Found 11 (81 requested) and removed 44 (44 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.13 3.39 Search for helices and strands: 0 residues in 0 chains, 10159 seeds are put forward NCS extension: 22 residues added (2 deleted due to clashes), 10181 seeds are put forward Round 1: 836 peptides, 112 chains. Longest chain 20 peptides. Score 0.610 Round 2: 952 peptides, 100 chains. Longest chain 38 peptides. Score 0.734 Round 3: 948 peptides, 102 chains. Longest chain 41 peptides. Score 0.725 Round 4: 942 peptides, 93 chains. Longest chain 44 peptides. Score 0.747 Round 5: 934 peptides, 104 chains. Longest chain 37 peptides. Score 0.711 Taking the results from Round 4 Chains 106, Residues 849, Estimated correctness of the model 74.5 % 24 chains (316 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 192 A and 200 A Built loop between residues 209 A and 216 A Built loop between residues 203 B and 210 B 100 chains (864 residues) following loop building 21 chains (335 residues) in sequence following loop building ------------------------------------------------------ Failed to save intermediate PDB 21957 reflections ( 99.70 % complete ) and 18950 restraints for refining 10194 atoms. 14377 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2356 (Rfree = 0.000) for 10194 atoms. Found 41 (82 requested) and removed 95 (45 requested) atoms. Cycle 7: After refmac, R = 0.2146 (Rfree = 0.000) for 10072 atoms. Found 22 (80 requested) and removed 53 (45 requested) atoms. Failed to save intermediate PDB Cycle 8: After refmac, R = 0.2108 (Rfree = 0.000) for 9999 atoms. Found 25 (77 requested) and removed 47 (45 requested) atoms. Cycle 9: After refmac, R = 0.2033 (Rfree = 0.000) for 9959 atoms. Found 10 (75 requested) and removed 44 (44 requested) atoms. Cycle 10: After refmac, R = 0.2014 (Rfree = 0.000) for 9906 atoms. Found 20 (73 requested) and removed 44 (44 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.13 3.39 Search for helices and strands: 0 residues in 0 chains, 10203 seeds are put forward NCS extension: 103 residues added (50 deleted due to clashes), 10306 seeds are put forward Round 1: 815 peptides, 107 chains. Longest chain 26 peptides. Score 0.611 Round 2: 921 peptides, 105 chains. Longest chain 36 peptides. Score 0.699 Round 3: 899 peptides, 106 chains. Longest chain 29 peptides. Score 0.680 Round 4: 907 peptides, 99 chains. Longest chain 37 peptides. Score 0.708 Round 5: 925 peptides, 99 chains. Longest chain 28 peptides. Score 0.720 Taking the results from Round 5 Chains 108, Residues 826, Estimated correctness of the model 69.3 % 16 chains (172 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 167 B and 178 B Built loop between residues 244 B and 249 B Built loop between residues 259 B and 264 B 106 chains (835 residues) following loop building 13 chains (190 residues) in sequence following loop building ------------------------------------------------------ 21957 reflections ( 99.70 % complete ) and 20837 restraints for refining 10196 atoms. 17096 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2327 (Rfree = 0.000) for 10196 atoms. Found 73 (73 requested) and removed 88 (45 requested) atoms. Failed to save intermediate PDB Cycle 12: After refmac, R = 0.2095 (Rfree = 0.000) for 10131 atoms. Found 37 (71 requested) and removed 56 (45 requested) atoms. Cycle 13: After refmac, R = 0.2014 (Rfree = 0.000) for 10079 atoms. Found 19 (68 requested) and removed 51 (45 requested) atoms. Cycle 14: After refmac, R = 0.1974 (Rfree = 0.000) for 10034 atoms. Found 21 (67 requested) and removed 50 (45 requested) atoms. Cycle 15: After refmac, R = 0.1929 (Rfree = 0.000) for 9992 atoms. Found 19 (64 requested) and removed 44 (44 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.13 3.39 Search for helices and strands: 0 residues in 0 chains, 10296 seeds are put forward NCS extension: 25 residues added (15 deleted due to clashes), 10321 seeds are put forward Round 1: 779 peptides, 112 chains. Longest chain 18 peptides. Score 0.559 Round 2: 828 peptides, 103 chains. Longest chain 23 peptides. Score 0.637 Round 3: 857 peptides, 109 chains. Longest chain 21 peptides. Score 0.638 Round 4: 840 peptides, 108 chains. Longest chain 22 peptides. Score 0.628 Round 5: 833 peptides, 107 chains. Longest chain 29 peptides. Score 0.626 Taking the results from Round 3 Chains 117, Residues 748, Estimated correctness of the model 50.9 % 18 chains (161 residues) have been docked in sequence ------------------------------------------------------ 21957 reflections ( 99.70 % complete ) and 21437 restraints for refining 10196 atoms. 18100 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2081 (Rfree = 0.000) for 10196 atoms. Found 57 (64 requested) and removed 59 (45 requested) atoms. Cycle 17: After refmac, R = 0.1983 (Rfree = 0.000) for 10168 atoms. Found 24 (64 requested) and removed 50 (45 requested) atoms. Cycle 18: After refmac, R = 0.1922 (Rfree = 0.000) for 10128 atoms. Found 28 (64 requested) and removed 45 (45 requested) atoms. Cycle 19: After refmac, R = 0.1878 (Rfree = 0.000) for 10104 atoms. Found 20 (63 requested) and removed 45 (45 requested) atoms. Cycle 20: After refmac, R = 0.1818 (Rfree = 0.000) for 10069 atoms. Found 19 (63 requested) and removed 45 (45 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.14 3.40 Search for helices and strands: 0 residues in 0 chains, 10345 seeds are put forward NCS extension: 27 residues added (6 deleted due to clashes), 10372 seeds are put forward Round 1: 731 peptides, 112 chains. Longest chain 26 peptides. Score 0.513 Round 2: 804 peptides, 104 chains. Longest chain 30 peptides. Score 0.613 Round 3: 805 peptides, 102 chains. Longest chain 25 peptides. Score 0.622 Round 4: 817 peptides, 104 chains. Longest chain 21 peptides. Score 0.624 Round 5: 788 peptides, 98 chains. Longest chain 30 peptides. Score 0.623 Taking the results from Round 4 Chains 106, Residues 713, Estimated correctness of the model 47.4 % 9 chains (84 residues) have been docked in sequence ------------------------------------------------------ 21957 reflections ( 99.70 % complete ) and 22353 restraints for refining 10196 atoms. 19319 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2068 (Rfree = 0.000) for 10196 atoms. Found 62 (64 requested) and removed 53 (45 requested) atoms. Cycle 22: After refmac, R = 0.1979 (Rfree = 0.000) for 10186 atoms. Found 24 (64 requested) and removed 48 (45 requested) atoms. Failed to save intermediate PDBFailed to save intermediate PDB Cycle 23: After refmac, R = 0.1937 (Rfree = 0.000) for 10150 atoms. Found 16 (64 requested) and removed 46 (45 requested) atoms. Cycle 24: After refmac, R = 0.1865 (Rfree = 0.000) for 10109 atoms. Found 18 (63 requested) and removed 47 (45 requested) atoms. Cycle 25: After refmac, R = 0.1833 (Rfree = 0.000) for 10064 atoms. Found 21 (63 requested) and removed 45 (45 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.15 3.41 Search for helices and strands: 0 residues in 0 chains, 10332 seeds are put forward NCS extension: 19 residues added (2 deleted due to clashes), 10351 seeds are put forward Round 1: 682 peptides, 109 chains. Longest chain 14 peptides. Score 0.475 Round 2: 733 peptides, 105 chains. Longest chain 22 peptides. Score 0.545 Round 3: 749 peptides, 99 chains. Longest chain 23 peptides. Score 0.585 Round 4: 753 peptides, 99 chains. Longest chain 30 peptides. Score 0.588 Round 5: 753 peptides, 98 chains. Longest chain 21 peptides. Score 0.592 Taking the results from Round 5 Chains 102, Residues 655, Estimated correctness of the model 38.9 % 10 chains (77 residues) have been docked in sequence ------------------------------------------------------ 21957 reflections ( 99.70 % complete ) and 22763 restraints for refining 10196 atoms. 20035 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2055 (Rfree = 0.000) for 10196 atoms. Found 45 (64 requested) and removed 54 (45 requested) atoms. Failed to save intermediate PDB Cycle 27: After refmac, R = 0.1960 (Rfree = 0.000) for 10157 atoms. Found 23 (64 requested) and removed 48 (45 requested) atoms. Cycle 28: After refmac, R = 0.1891 (Rfree = 0.000) for 10125 atoms. Found 26 (63 requested) and removed 46 (45 requested) atoms. Failed to save intermediate PDB Cycle 29: After refmac, R = 0.1748 (Rfree = 0.000) for 10099 atoms. Found 11 (63 requested) and removed 45 (45 requested) atoms. Cycle 30: After refmac, R = 0.1727 (Rfree = 0.000) for 10062 atoms. Found 13 (63 requested) and removed 45 (45 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.18 3.45 Search for helices and strands: 0 residues in 0 chains, 10322 seeds are put forward NCS extension: 16 residues added (2 deleted due to clashes), 10338 seeds are put forward Round 1: 650 peptides, 107 chains. Longest chain 23 peptides. Score 0.450 Round 2: 720 peptides, 101 chains. Longest chain 23 peptides. Score 0.549 Round 3: 745 peptides, 109 chains. Longest chain 27 peptides. Score 0.539 Round 4: 732 peptides, 95 chains. Longest chain 23 peptides. Score 0.585 Round 5: 705 peptides, 93 chains. Longest chain 38 peptides. Score 0.569 Taking the results from Round 4 Chains 103, Residues 637, Estimated correctness of the model 37.0 % 11 chains (92 residues) have been docked in sequence ------------------------------------------------------ 21957 reflections ( 99.70 % complete ) and 22499 restraints for refining 10196 atoms. 19778 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2118 (Rfree = 0.000) for 10196 atoms. Found 57 (64 requested) and removed 55 (45 requested) atoms. Cycle 32: After refmac, R = 0.1965 (Rfree = 0.000) for 10174 atoms. Found 28 (64 requested) and removed 45 (45 requested) atoms. Cycle 33: After refmac, R = 0.1897 (Rfree = 0.000) for 10148 atoms. Found 16 (64 requested) and removed 45 (45 requested) atoms. Cycle 34: After refmac, R = 0.1888 (Rfree = 0.000) for 10115 atoms. Found 12 (63 requested) and removed 46 (45 requested) atoms. Cycle 35: After refmac, R = 0.1864 (Rfree = 0.000) for 10075 atoms. Found 19 (63 requested) and removed 45 (45 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.17 3.44 Search for helices and strands: 0 residues in 0 chains, 10323 seeds are put forward NCS extension: 15 residues added (0 deleted due to clashes), 10338 seeds are put forward Round 1: 600 peptides, 101 chains. Longest chain 18 peptides. Score 0.423 Round 2: 684 peptides, 92 chains. Longest chain 25 peptides. Score 0.553 Round 3: 715 peptides, 98 chains. Longest chain 24 peptides. Score 0.557 Round 4: 700 peptides, 100 chains. Longest chain 28 peptides. Score 0.534 Round 5: 692 peptides, 89 chains. Longest chain 32 peptides. Score 0.574 Taking the results from Round 5 Chains 93, Residues 603, Estimated correctness of the model 33.9 % 11 chains (81 residues) have been docked in sequence ------------------------------------------------------ 21957 reflections ( 99.70 % complete ) and 22695 restraints for refining 10196 atoms. 20131 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2021 (Rfree = 0.000) for 10196 atoms. Found 46 (64 requested) and removed 57 (45 requested) atoms. Cycle 37: After refmac, R = 0.1937 (Rfree = 0.000) for 10167 atoms. Found 23 (64 requested) and removed 48 (45 requested) atoms. Failed to save intermediate PDB Cycle 38: After refmac, R = 0.1865 (Rfree = 0.000) for 10134 atoms. Found 21 (64 requested) and removed 45 (45 requested) atoms. Cycle 39: After refmac, R = 0.1833 (Rfree = 0.000) for 10102 atoms. Found 11 (63 requested) and removed 45 (45 requested) atoms. Cycle 40: After refmac, R = 0.1810 (Rfree = 0.000) for 10058 atoms. Found 14 (63 requested) and removed 45 (45 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.17 3.44 Search for helices and strands: 0 residues in 0 chains, 10315 seeds are put forward NCS extension: 23 residues added (2 deleted due to clashes), 10338 seeds are put forward Round 1: 598 peptides, 101 chains. Longest chain 17 peptides. Score 0.420 Round 2: 698 peptides, 103 chains. Longest chain 19 peptides. Score 0.519 Round 3: 674 peptides, 103 chains. Longest chain 20 peptides. Score 0.494 Round 4: 686 peptides, 97 chains. Longest chain 23 peptides. Score 0.533 Round 5: 664 peptides, 93 chains. Longest chain 20 peptides. Score 0.529 Taking the results from Round 4 Chains 99, Residues 589, Estimated correctness of the model 21.7 % 6 chains (40 residues) have been docked in sequence ------------------------------------------------------ 21957 reflections ( 99.70 % complete ) and 23187 restraints for refining 10195 atoms. 20825 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1937 (Rfree = 0.000) for 10195 atoms. Found 56 (64 requested) and removed 54 (45 requested) atoms. Cycle 42: After refmac, R = 0.1845 (Rfree = 0.000) for 10175 atoms. Found 25 (64 requested) and removed 47 (45 requested) atoms. Failed to save intermediate PDB Cycle 43: After refmac, R = 0.1813 (Rfree = 0.000) for 10148 atoms. Found 31 (64 requested) and removed 45 (45 requested) atoms. Cycle 44: After refmac, R = 0.1778 (Rfree = 0.000) for 10125 atoms. Found 36 (63 requested) and removed 45 (45 requested) atoms. Cycle 45: After refmac, R = 0.1732 (Rfree = 0.000) for 10111 atoms. Found 30 (63 requested) and removed 45 (45 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.17 3.44 Search for helices and strands: 0 residues in 0 chains, 10346 seeds are put forward NCS extension: 32 residues added (0 deleted due to clashes), 10378 seeds are put forward Round 1: 511 peptides, 91 chains. Longest chain 20 peptides. Score 0.368 Round 2: 590 peptides, 91 chains. Longest chain 19 peptides. Score 0.460 Round 3: 574 peptides, 88 chains. Longest chain 20 peptides. Score 0.457 Round 4: 562 peptides, 83 chains. Longest chain 21 peptides. Score 0.468 Round 5: 565 peptides, 82 chains. Longest chain 22 peptides. Score 0.477 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 82, Residues 483, Estimated correctness of the model 3.7 % 4 chains (21 residues) have been docked in sequence Sequence coverage is 4 % Consider running further cycles of model building using 2obn-3_warpNtrace.pdb as input Building loops using Loopy2018 82 chains (483 residues) following loop building 4 chains (21 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 21957 reflections ( 99.70 % complete ) and 23847 restraints for refining 10196 atoms. 21944 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1869 (Rfree = 0.000) for 10196 atoms. Found 0 (64 requested) and removed 43 (45 requested) atoms. Failed to save intermediate PDB Cycle 47: After refmac, R = 0.1795 (Rfree = 0.000) for 10145 atoms. Found 0 (64 requested) and removed 13 (45 requested) atoms. Failed to save intermediate PDB Cycle 48: After refmac, R = 0.1775 (Rfree = 0.000) for 10126 atoms. Found 0 (63 requested) and removed 13 (45 requested) atoms. Failed to save intermediate PDB Cycle 49: After refmac, R = 0.1774 (Rfree = 0.000) for 10110 atoms. Found 0 (63 requested) and removed 11 (45 requested) atoms. Writing output files ... Failed to save intermediate PDB Normal termination of warpNtrace Tue 25 Dec 21:44:58 GMT 2018 Job finished. TimeTaking 137.04