Tue 25 Dec 19:27:57 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 2hq7-3.2-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2hq7-3.2-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2hq7-3.2-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2hq7-3.2-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/2hq7-3.2-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2hq7-3.2-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 19:28:07 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/2hq7-3.2-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2hq7-3.2-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 199 and 0 Target number of residues in the AU: 199 Target solvent content: 0.6197 Checking the provided sequence file Detected sequence length: 146 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 292 Adjusted target solvent content: 0.44 Input MTZ file: 2hq7-3.2-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: 5 Cell parameters: 85.850 36.790 97.970 90.000 113.753 90.000 Input sequence file: 2hq7-3.2-parrot-hancs.fasta_lf Building free atoms model in initial map for 2336 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 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: 89.671 3.200 Wilson plot Bfac: 61.20 4803 reflections ( 99.48 % complete ) and 0 restraints for refining 2592 atoms. Observations/parameters ratio is 0.46 ------------------------------------------------------ Starting model: R = 0.3039 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2407 (Rfree = 0.000) for 2592 atoms. Found 23 (23 requested) and removed 18 (11 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.10 3.36 Search for helices and strands: 0 residues in 0 chains, 2655 seeds are put forward NCS extension: 0 residues added, 2655 seeds are put forward Round 1: 148 peptides, 24 chains. Longest chain 11 peptides. Score 0.476 Round 2: 185 peptides, 23 chains. Longest chain 20 peptides. Score 0.656 Round 3: 206 peptides, 22 chains. Longest chain 27 peptides. Score 0.739 Round 4: 214 peptides, 18 chains. Longest chain 31 peptides. Score 0.806 Round 5: 218 peptides, 18 chains. Longest chain 29 peptides. Score 0.814 Taking the results from Round 5 Chains 18, Residues 200, Estimated correctness of the model 85.5 % 1 chains (13 residues) have been docked in sequence ------------------------------------------------------ 4803 reflections ( 99.48 % complete ) and 4301 restraints for refining 2133 atoms. 3461 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2394 (Rfree = 0.000) for 2133 atoms. Found 16 (19 requested) and removed 16 (9 requested) atoms. Cycle 2: After refmac, R = 0.2131 (Rfree = 0.000) for 2117 atoms. Found 6 (19 requested) and removed 10 (9 requested) atoms. Failed to save intermediate PDB Cycle 3: After refmac, R = 0.2146 (Rfree = 0.000) for 2107 atoms. Found 4 (17 requested) and removed 9 (9 requested) atoms. Cycle 4: After refmac, R = 0.2068 (Rfree = 0.000) for 2097 atoms. Found 3 (17 requested) and removed 9 (9 requested) atoms. Cycle 5: After refmac, R = 0.2069 (Rfree = 0.000) for 2086 atoms. Found 1 (17 requested) and removed 9 (9 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.17 3.44 Search for helices and strands: 0 residues in 0 chains, 2136 seeds are put forward NCS extension: 11 residues added (2 deleted due to clashes), 2147 seeds are put forward Round 1: 186 peptides, 21 chains. Longest chain 22 peptides. Score 0.692 Round 2: 192 peptides, 17 chains. Longest chain 25 peptides. Score 0.765 Round 3: 198 peptides, 15 chains. Longest chain 30 peptides. Score 0.804 Round 4: 211 peptides, 17 chains. Longest chain 32 peptides. Score 0.810 Round 5: 212 peptides, 18 chains. Longest chain 22 peptides. Score 0.802 Taking the results from Round 4 Chains 18, Residues 194, Estimated correctness of the model 84.9 % 2 chains (44 residues) have been docked in sequence Building loops using Loopy2018 18 chains (194 residues) following loop building 2 chains (44 residues) in sequence following loop building ------------------------------------------------------ 4803 reflections ( 99.48 % complete ) and 4174 restraints for refining 2133 atoms. 3242 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2332 (Rfree = 0.000) for 2133 atoms. Found 15 (17 requested) and removed 16 (9 requested) atoms. Cycle 7: After refmac, R = 0.2510 (Rfree = 0.000) for 2120 atoms. Found 10 (17 requested) and removed 13 (9 requested) atoms. Failed to save intermediate PDB Cycle 8: After refmac, R = 0.2579 (Rfree = 0.000) for 2106 atoms. Found 15 (15 requested) and removed 18 (9 requested) atoms. Cycle 9: After refmac, R = 0.2609 (Rfree = 0.000) for 2096 atoms. Found 15 (15 requested) and removed 19 (9 requested) atoms. Cycle 10: After refmac, R = 0.2384 (Rfree = 0.000) for 2087 atoms. Found 15 (15 requested) and removed 17 (9 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.15 3.41 Search for helices and strands: 0 residues in 0 chains, 2155 seeds are put forward NCS extension: 21 residues added (18 deleted due to clashes), 2176 seeds are put forward Round 1: 192 peptides, 21 chains. Longest chain 18 peptides. Score 0.711 Round 2: 202 peptides, 20 chains. Longest chain 19 peptides. Score 0.754 Round 3: 207 peptides, 15 chains. Longest chain 31 peptides. Score 0.823 Round 4: 204 peptides, 17 chains. Longest chain 33 peptides. Score 0.795 Round 5: 202 peptides, 19 chains. Longest chain 25 peptides. Score 0.766 Taking the results from Round 3 Chains 15, Residues 192, Estimated correctness of the model 86.7 % 1 chains (30 residues) have been docked in sequence ------------------------------------------------------ 4803 reflections ( 99.48 % complete ) and 4211 restraints for refining 2133 atoms. 3347 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2103 (Rfree = 0.000) for 2133 atoms. Found 14 (15 requested) and removed 19 (9 requested) atoms. Cycle 12: After refmac, R = 0.1887 (Rfree = 0.000) for 2126 atoms. Found 3 (15 requested) and removed 12 (9 requested) atoms. Cycle 13: After refmac, R = 0.1813 (Rfree = 0.000) for 2116 atoms. Found 5 (14 requested) and removed 9 (9 requested) atoms. Failed to save intermediate PDB Cycle 14: After refmac, R = 0.1777 (Rfree = 0.000) for 2111 atoms. Found 5 (13 requested) and removed 9 (9 requested) atoms. Cycle 15: After refmac, R = 0.1767 (Rfree = 0.000) for 2104 atoms. Found 7 (13 requested) and removed 9 (9 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.15 3.41 Search for helices and strands: 0 residues in 0 chains, 2162 seeds are put forward NCS extension: 27 residues added (8 deleted due to clashes), 2189 seeds are put forward Round 1: 184 peptides, 20 chains. Longest chain 19 peptides. Score 0.700 Round 2: 205 peptides, 21 chains. Longest chain 31 peptides. Score 0.749 Round 3: 200 peptides, 22 chains. Longest chain 28 peptides. Score 0.721 Round 4: 211 peptides, 15 chains. Longest chain 62 peptides. Score 0.831 Round 5: 202 peptides, 17 chains. Longest chain 29 peptides. Score 0.790 Taking the results from Round 4 Chains 20, Residues 196, Estimated correctness of the model 87.8 % 4 chains (91 residues) have been docked in sequence Building loops using Loopy2018 20 chains (196 residues) following loop building 4 chains (91 residues) in sequence following loop building ------------------------------------------------------ Failed to save intermediate PDB 4803 reflections ( 99.48 % complete ) and 3587 restraints for refining 2133 atoms. 2454 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2140 (Rfree = 0.000) for 2133 atoms. Found 13 (13 requested) and removed 17 (9 requested) atoms. Failed to save intermediate PDB Cycle 17: After refmac, R = 0.2247 (Rfree = 0.000) for 2114 atoms. Found 13 (13 requested) and removed 12 (9 requested) atoms. Failed to save intermediate PDB Cycle 18: After refmac, R = 0.2047 (Rfree = 0.000) for 2105 atoms. Found 8 (12 requested) and removed 12 (9 requested) atoms. Cycle 19: After refmac, R = 0.1757 (Rfree = 0.000) for 2094 atoms. Found 4 (12 requested) and removed 11 (9 requested) atoms. Failed to save intermediate PDB Cycle 20: After refmac, R = 0.1698 (Rfree = 0.000) for 2083 atoms. Found 8 (11 requested) and removed 9 (9 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.13 3.39 Search for helices and strands: 0 residues in 0 chains, 2167 seeds are put forward NCS extension: 41 residues added (17 deleted due to clashes), 2208 seeds are put forward Round 1: 189 peptides, 23 chains. Longest chain 13 peptides. Score 0.671 Round 2: 208 peptides, 23 chains. Longest chain 30 peptides. Score 0.731 Round 3: 200 peptides, 22 chains. Longest chain 18 peptides. Score 0.721 Round 4: 190 peptides, 20 chains. Longest chain 22 peptides. Score 0.719 Round 5: 194 peptides, 21 chains. Longest chain 17 peptides. Score 0.717 Taking the results from Round 2 Chains 23, Residues 185, Estimated correctness of the model 71.5 % 1 chains (29 residues) have been docked in sequence ------------------------------------------------------ 4803 reflections ( 99.48 % complete ) and 4393 restraints for refining 2133 atoms. 3558 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 21: After refmac, R = 0.1985 (Rfree = 0.000) for 2133 atoms. Found 9 (11 requested) and removed 14 (9 requested) atoms. Cycle 22: After refmac, R = 0.1915 (Rfree = 0.000) for 2126 atoms. Found 6 (11 requested) and removed 10 (9 requested) atoms. Cycle 23: After refmac, R = 0.1818 (Rfree = 0.000) for 2119 atoms. Found 6 (11 requested) and removed 10 (9 requested) atoms. Cycle 24: After refmac, R = 0.1776 (Rfree = 0.000) for 2113 atoms. Found 1 (10 requested) and removed 9 (9 requested) atoms. Cycle 25: After refmac, R = 0.1753 (Rfree = 0.000) for 2105 atoms. Found 0 (9 requested) and removed 9 (9 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.13 3.39 Search for helices and strands: 0 residues in 0 chains, 2169 seeds are put forward NCS extension: 15 residues added (0 deleted due to clashes), 2184 seeds are put forward Round 1: 180 peptides, 20 chains. Longest chain 17 peptides. Score 0.687 Round 2: 193 peptides, 18 chains. Longest chain 19 peptides. Score 0.755 Round 3: 193 peptides, 17 chains. Longest chain 31 peptides. Score 0.768 Round 4: 193 peptides, 15 chains. Longest chain 31 peptides. Score 0.792 Round 5: 185 peptides, 17 chains. Longest chain 31 peptides. Score 0.746 Taking the results from Round 4 Chains 15, Residues 178, Estimated correctness of the model 82.2 % 2 chains (55 residues) have been docked in sequence Building loops using Loopy2018 15 chains (178 residues) following loop building 2 chains (55 residues) in sequence following loop building ------------------------------------------------------ Failed to save intermediate PDB 4803 reflections ( 99.48 % complete ) and 4043 restraints for refining 2133 atoms. 3102 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2093 (Rfree = 0.000) for 2133 atoms. Found 9 (9 requested) and removed 15 (9 requested) atoms. Cycle 27: After refmac, R = 0.2718 (Rfree = 0.000) for 2123 atoms. Found 9 (9 requested) and removed 13 (9 requested) atoms. Failed to save intermediate PDB Cycle 28: After refmac, R = 0.2121 (Rfree = 0.000) for 2108 atoms. Found 9 (9 requested) and removed 10 (9 requested) atoms. Cycle 29: After refmac, R = 0.2204 (Rfree = 0.000) for 2104 atoms. Found 9 (9 requested) and removed 11 (9 requested) atoms. Failed to save intermediate PDB Cycle 30: After refmac, R = 0.1755 (Rfree = 0.000) for 2097 atoms. Found 9 (9 requested) and removed 10 (9 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.13 3.39 Search for helices and strands: 0 residues in 0 chains, 2154 seeds are put forward NCS extension: 17 residues added (10 deleted due to clashes), 2171 seeds are put forward Round 1: 183 peptides, 21 chains. Longest chain 24 peptides. Score 0.681 Round 2: 200 peptides, 21 chains. Longest chain 28 peptides. Score 0.735 Round 3: 206 peptides, 20 chains. Longest chain 29 peptides. Score 0.764 Round 4: 194 peptides, 18 chains. Longest chain 29 peptides. Score 0.758 Round 5: 193 peptides, 19 chains. Longest chain 32 peptides. Score 0.742 Taking the results from Round 3 Chains 21, Residues 186, Estimated correctness of the model 77.6 % 2 chains (47 residues) have been docked in sequence Building loops using Loopy2018 21 chains (186 residues) following loop building 2 chains (47 residues) in sequence following loop building ------------------------------------------------------ 4803 reflections ( 99.48 % complete ) and 4086 restraints for refining 2133 atoms. 3170 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1915 (Rfree = 0.000) for 2133 atoms. Found 8 (9 requested) and removed 15 (9 requested) atoms. Cycle 32: After refmac, R = 0.1761 (Rfree = 0.000) for 2125 atoms. Found 4 (9 requested) and removed 9 (9 requested) atoms. Failed to save intermediate PDB Cycle 33: After refmac, R = 0.1719 (Rfree = 0.000) for 2120 atoms. Found 1 (9 requested) and removed 9 (9 requested) atoms. Failed to save intermediate PDB Cycle 34: After refmac, R = 0.1725 (Rfree = 0.000) for 2112 atoms. Found 1 (9 requested) and removed 9 (9 requested) atoms. Cycle 35: After refmac, R = 0.1664 (Rfree = 0.000) for 2104 atoms. Found 2 (9 requested) and removed 9 (9 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.17 3.44 Search for helices and strands: 0 residues in 0 chains, 2156 seeds are put forward NCS extension: 28 residues added (9 deleted due to clashes), 2184 seeds are put forward Round 1: 180 peptides, 23 chains. Longest chain 17 peptides. Score 0.638 Round 2: 192 peptides, 19 chains. Longest chain 31 peptides. Score 0.739 Round 3: 205 peptides, 16 chains. Longest chain 41 peptides. Score 0.808 Round 4: 195 peptides, 20 chains. Longest chain 43 peptides. Score 0.734 Round 5: 192 peptides, 18 chains. Longest chain 34 peptides. Score 0.752 Taking the results from Round 3 Chains 19, Residues 189, Estimated correctness of the model 84.6 % 2 chains (52 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 91 A and 102 A 16 chains (192 residues) following loop building 1 chains (62 residues) in sequence following loop building ------------------------------------------------------ 4803 reflections ( 99.48 % complete ) and 3823 restraints for refining 2133 atoms. 2808 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2087 (Rfree = 0.000) for 2133 atoms. Found 9 (9 requested) and removed 20 (9 requested) atoms. Cycle 37: After refmac, R = 0.1893 (Rfree = 0.000) for 2117 atoms. Found 6 (9 requested) and removed 13 (9 requested) atoms. Cycle 38: After refmac, R = 0.1865 (Rfree = 0.000) for 2106 atoms. Found 6 (9 requested) and removed 9 (9 requested) atoms. Failed to save intermediate PDB Cycle 39: After refmac, R = 0.2027 (Rfree = 0.000) for 2103 atoms. Found 9 (9 requested) and removed 9 (9 requested) atoms. Cycle 40: After refmac, R = 0.1721 (Rfree = 0.000) for 2101 atoms. Found 8 (9 requested) and removed 11 (9 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.16 3.42 Search for helices and strands: 0 residues in 0 chains, 2172 seeds are put forward NCS extension: 79 residues added (27 deleted due to clashes), 2251 seeds are put forward Round 1: 170 peptides, 20 chains. Longest chain 16 peptides. Score 0.651 Round 2: 184 peptides, 18 chains. Longest chain 29 peptides. Score 0.729 Round 3: 180 peptides, 20 chains. Longest chain 21 peptides. Score 0.687 Round 4: 177 peptides, 18 chains. Longest chain 22 peptides. Score 0.708 Round 5: 174 peptides, 20 chains. Longest chain 21 peptides. Score 0.666 Taking the results from Round 2 Chains 20, Residues 166, Estimated correctness of the model 71.1 % 2 chains (38 residues) have been docked in sequence Building loops using Loopy2018 20 chains (166 residues) following loop building 2 chains (38 residues) in sequence following loop building ------------------------------------------------------ 4803 reflections ( 99.48 % complete ) and 4233 restraints for refining 2133 atoms. 3426 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1924 (Rfree = 0.000) for 2133 atoms. Found 9 (9 requested) and removed 12 (9 requested) atoms. Failed to save intermediate PDB Cycle 42: After refmac, R = 0.1852 (Rfree = 0.000) for 2128 atoms. Found 7 (9 requested) and removed 10 (9 requested) atoms. Cycle 43: After refmac, R = 0.1769 (Rfree = 0.000) for 2125 atoms. Found 3 (9 requested) and removed 9 (9 requested) atoms. Failed to save intermediate PDB Cycle 44: After refmac, R = 0.1705 (Rfree = 0.000) for 2118 atoms. Found 3 (9 requested) and removed 9 (9 requested) atoms. Cycle 45: After refmac, R = 0.1604 (Rfree = 0.000) for 2109 atoms. Found 8 (9 requested) and removed 9 (9 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.16 3.42 Search for helices and strands: 0 residues in 0 chains, 2165 seeds are put forward NCS extension: 38 residues added (6 deleted due to clashes), 2203 seeds are put forward Round 1: 166 peptides, 19 chains. Longest chain 16 peptides. Score 0.653 Round 2: 171 peptides, 14 chains. Longest chain 26 peptides. Score 0.748 Round 3: 179 peptides, 19 chains. Longest chain 16 peptides. Score 0.699 Round 4: 174 peptides, 16 chains. Longest chain 30 peptides. Score 0.728 Round 5: 171 peptides, 18 chains. Longest chain 22 peptides. Score 0.688 Taking the results from Round 2 Last building cycle: Chain fragments will be rearranged Chains 16, Residues 157, Estimated correctness of the model 74.7 % 2 chains (39 residues) have been docked in sequence Sequence coverage is 24 % Consider running further cycles of model building using 2hq7-3_warpNtrace.pdb as input Building loops using Loopy2018 16 chains (157 residues) following loop building 2 chains (39 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 4803 reflections ( 99.48 % complete ) and 4217 restraints for refining 2133 atoms. 3452 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1780 (Rfree = 0.000) for 2133 atoms. Found 0 (9 requested) and removed 7 (9 requested) atoms. Failed to save intermediate PDB Cycle 47: After refmac, R = 0.1736 (Rfree = 0.000) for 2121 atoms. Found 0 (9 requested) and removed 0 (9 requested) atoms. Failed to save intermediate PDB Cycle 48: After refmac, R = 0.1710 (Rfree = 0.000) for 2120 atoms. Found 0 (9 requested) and removed 0 (9 requested) atoms. Cycle 49: After refmac, R = 0.1727 (Rfree = 0.000) for 2118 atoms. Found 0 (9 requested) and removed 1 (9 requested) atoms. Writing output files ... Normal termination of warpNtrace Tue 25 Dec 20:15:37 GMT 2018 Job finished. TimeTaking 47.68