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 1vr3-2.1-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/1vr3-2.1-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/1vr3-2.1-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vr3-2.1-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/1vr3-2.1-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vr3-2.1-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/1vr3-2.1-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vr3-2.1-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 303 and 0 Target number of residues in the AU: 303 Target solvent content: 0.5411 Checking the provided sequence file Detected sequence length: 191 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 382 Adjusted target solvent content: 0.42 Input MTZ file: 1vr3-2.1-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: 92 Cell parameters: 79.137 79.137 114.115 90.000 90.000 90.000 Input sequence file: 1vr3-2.1-parrot-hancs.fasta_lf Building free atoms model in initial map for 3056 target number of atoms Had to go as low as 0.35 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 1 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: 65.030 2.060 Wilson plot Bfac: 32.93 23087 reflections ( 99.94 % complete ) and 0 restraints for refining 3387 atoms. Observations/parameters ratio is 1.70 ------------------------------------------------------ Starting model: R = 0.3144 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2482 (Rfree = 0.000) for 3387 atoms. Found 95 (106 requested) and removed 116 (53 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 2.28 2.54 NCS extension: 0 residues added, 3366 seeds are put forward Round 1: 148 peptides, 14 chains. Longest chain 34 peptides. Score 0.606 Round 2: 162 peptides, 10 chains. Longest chain 58 peptides. Score 0.710 Round 3: 162 peptides, 10 chains. Longest chain 54 peptides. Score 0.710 Round 4: 173 peptides, 5 chains. Longest chain 86 peptides. Score 0.799 Round 5: 174 peptides, 5 chains. Longest chain 92 peptides. Score 0.800 Taking the results from Round 5 Chains 6, Residues 169, Estimated correctness of the model 95.9 % 3 chains (149 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 33 A and 44 A 4 chains (173 residues) following loop building 2 chains (159 residues) in sequence following loop building ------------------------------------------------------ 23087 reflections ( 99.94 % complete ) and 4049 restraints for refining 2852 atoms. 2614 conditional restraints added. Observations/parameters ratio is 2.02 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3007 (Rfree = 0.000) for 2852 atoms. Found 90 (90 requested) and removed 77 (45 requested) atoms. Cycle 2: After refmac, R = 0.2736 (Rfree = 0.000) for 2812 atoms. Found 70 (88 requested) and removed 49 (45 requested) atoms. Cycle 3: After refmac, R = 0.2421 (Rfree = 0.000) for 2769 atoms. Found 56 (85 requested) and removed 49 (44 requested) atoms. Cycle 4: After refmac, R = 0.2272 (Rfree = 0.000) for 2692 atoms. Found 75 (82 requested) and removed 45 (43 requested) atoms. Failed to save intermediate PDB Cycle 5: After refmac, R = 0.2184 (Rfree = 0.000) for 2684 atoms. Found 57 (78 requested) and removed 42 (42 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 2.24 2.49 NCS extension: 0 residues added, 2699 seeds are put forward Round 1: 175 peptides, 5 chains. Longest chain 83 peptides. Score 0.802 Round 2: 176 peptides, 4 chains. Longest chain 118 peptides. Score 0.816 Round 3: 174 peptides, 4 chains. Longest chain 84 peptides. Score 0.812 Round 4: 175 peptides, 4 chains. Longest chain 95 peptides. Score 0.814 Round 5: 173 peptides, 2 chains. Longest chain 129 peptides. Score 0.832 Taking the results from Round 5 Chains 4, Residues 171, Estimated correctness of the model 97.0 % 3 chains (166 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 56 A and 59 A Built loop between residues 172 A and 179 A 1 chains (174 residues) following loop building 1 chains (174 residues) in sequence following loop building ------------------------------------------------------ 23087 reflections ( 99.94 % complete ) and 2722 restraints for refining 2422 atoms. 1198 conditional restraints added. Observations/parameters ratio is 2.38 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2459 (Rfree = 0.000) for 2422 atoms. Found 68 (68 requested) and removed 48 (38 requested) atoms. Cycle 7: After refmac, R = 0.2220 (Rfree = 0.000) for 2430 atoms. Found 67 (67 requested) and removed 38 (38 requested) atoms. Failed to save intermediate PDB Cycle 8: After refmac, R = 0.2139 (Rfree = 0.000) for 2434 atoms. Found 47 (66 requested) and removed 38 (38 requested) atoms. Cycle 9: After refmac, R = 0.2072 (Rfree = 0.000) for 2427 atoms. Found 51 (64 requested) and removed 39 (38 requested) atoms. Failed to save intermediate PDB Cycle 10: After refmac, R = 0.2016 (Rfree = 0.000) for 2401 atoms. Found 42 (62 requested) and removed 38 (38 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 2.26 2.52 NCS extension: 0 residues added, 2408 seeds are put forward Round 1: 170 peptides, 4 chains. Longest chain 78 peptides. Score 0.804 Round 2: 175 peptides, 4 chains. Longest chain 87 peptides. Score 0.814 Round 3: 174 peptides, 3 chains. Longest chain 77 peptides. Score 0.823 Round 4: 178 peptides, 2 chains. Longest chain 125 peptides. Score 0.840 Round 5: 173 peptides, 4 chains. Longest chain 132 peptides. Score 0.810 Taking the results from Round 4 Chains 5, Residues 176, Estimated correctness of the model 97.3 % 3 chains (168 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 61 B and 66 B Built loop between residues 169 B and 176 B 1 chains (178 residues) following loop building 1 chains (178 residues) in sequence following loop building ------------------------------------------------------ Failed to save intermediate PDB 23087 reflections ( 99.94 % complete ) and 2453 restraints for refining 2278 atoms. 901 conditional restraints added. Observations/parameters ratio is 2.53 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2275 (Rfree = 0.000) for 2278 atoms. Found 57 (57 requested) and removed 39 (35 requested) atoms. Cycle 12: After refmac, R = 0.2091 (Rfree = 0.000) for 2286 atoms. Found 53 (56 requested) and removed 36 (36 requested) atoms. Cycle 13: After refmac, R = 0.1991 (Rfree = 0.000) for 2293 atoms. Found 34 (55 requested) and removed 36 (36 requested) atoms. Failed to save intermediate PDB Cycle 14: After refmac, R = 0.1930 (Rfree = 0.000) for 2277 atoms. Found 35 (53 requested) and removed 36 (36 requested) atoms. Cycle 15: After refmac, R = 0.1865 (Rfree = 0.000) for 2262 atoms. Found 39 (51 requested) and removed 35 (35 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 2.24 2.49 NCS extension: 0 residues added, 2267 seeds are put forward Round 1: 174 peptides, 5 chains. Longest chain 87 peptides. Score 0.800 Round 2: 174 peptides, 4 chains. Longest chain 101 peptides. Score 0.812 Round 3: 177 peptides, 2 chains. Longest chain 132 peptides. Score 0.839 Round 4: 175 peptides, 4 chains. Longest chain 103 peptides. Score 0.814 Round 5: 177 peptides, 2 chains. Longest chain 90 peptides. Score 0.839 Taking the results from Round 5 Chains 4, Residues 175, Estimated correctness of the model 97.2 % 3 chains (170 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 98 A and 101 A Built loop between residues 169 A and 176 A 1 chains (178 residues) following loop building 1 chains (178 residues) in sequence following loop building ------------------------------------------------------ 23087 reflections ( 99.94 % complete ) and 2343 restraints for refining 2191 atoms. 791 conditional restraints added. Observations/parameters ratio is 2.63 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2263 (Rfree = 0.000) for 2191 atoms. Found 48 (48 requested) and removed 35 (34 requested) atoms. Cycle 17: After refmac, R = 0.2084 (Rfree = 0.000) for 2192 atoms. Found 47 (47 requested) and removed 36 (34 requested) atoms. Failed to save intermediate PDB Cycle 18: After refmac, R = 0.2005 (Rfree = 0.000) for 2196 atoms. Found 37 (46 requested) and removed 34 (34 requested) atoms. Cycle 19: After refmac, R = 0.1937 (Rfree = 0.000) for 2184 atoms. Found 44 (44 requested) and removed 34 (34 requested) atoms. Failed to save intermediate PDB Cycle 20: After refmac, R = 0.1859 (Rfree = 0.000) for 2186 atoms. Found 32 (43 requested) and removed 37 (34 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 2.24 2.49 NCS extension: 0 residues added, 2182 seeds are put forward Round 1: 176 peptides, 3 chains. Longest chain 139 peptides. Score 0.826 Round 2: 173 peptides, 4 chains. Longest chain 102 peptides. Score 0.810 Round 3: 173 peptides, 4 chains. Longest chain 84 peptides. Score 0.810 Round 4: 176 peptides, 8 chains. Longest chain 73 peptides. Score 0.770 Round 5: 174 peptides, 3 chains. Longest chain 134 peptides. Score 0.823 Taking the results from Round 1 Chains 4, Residues 173, Estimated correctness of the model 96.8 % 3 chains (172 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 32 A and 35 A Built loop between residues 172 A and 176 A 1 chains (177 residues) following loop building 1 chains (177 residues) in sequence following loop building ------------------------------------------------------ Failed to save intermediate PDB 23087 reflections ( 99.94 % complete ) and 2203 restraints for refining 2128 atoms. 659 conditional restraints added. Observations/parameters ratio is 2.71 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2169 (Rfree = 0.000) for 2128 atoms. Found 40 (40 requested) and removed 37 (33 requested) atoms. Failed to save intermediate PDB Cycle 22: After refmac, R = 0.2039 (Rfree = 0.000) for 2120 atoms. Found 39 (39 requested) and removed 34 (33 requested) atoms. Failed to save intermediate PDB Cycle 23: After refmac, R = 0.1957 (Rfree = 0.000) for 2118 atoms. Found 34 (37 requested) and removed 33 (33 requested) atoms. Cycle 24: After refmac, R = 0.1900 (Rfree = 0.000) for 2111 atoms. Found 34 (36 requested) and removed 35 (33 requested) atoms. Cycle 25: After refmac, R = 0.1902 (Rfree = 0.000) for 2098 atoms. Found 34 (34 requested) and removed 33 (33 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 2.24 2.49 NCS extension: 0 residues added, 2101 seeds are put forward Round 1: 174 peptides, 4 chains. Longest chain 139 peptides. Score 0.812 Round 2: 173 peptides, 3 chains. Longest chain 102 peptides. Score 0.821 Round 3: 176 peptides, 3 chains. Longest chain 148 peptides. Score 0.826 Round 4: 176 peptides, 4 chains. Longest chain 78 peptides. Score 0.816 Round 5: 169 peptides, 6 chains. Longest chain 70 peptides. Score 0.778 Taking the results from Round 3 Chains 5, Residues 173, Estimated correctness of the model 96.8 % 3 chains (166 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 23 A and 30 A Built loop between residues 169 A and 175 A 1 chains (177 residues) following loop building 1 chains (177 residues) in sequence following loop building ------------------------------------------------------ 23087 reflections ( 99.94 % complete ) and 2084 restraints for refining 2068 atoms. 540 conditional restraints added. Observations/parameters ratio is 2.79 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2218 (Rfree = 0.000) for 2068 atoms. Found 32 (32 requested) and removed 36 (32 requested) atoms. Failed to save intermediate PDB Cycle 27: After refmac, R = 0.2059 (Rfree = 0.000) for 2055 atoms. Found 32 (32 requested) and removed 32 (32 requested) atoms. Cycle 28: After refmac, R = 0.1979 (Rfree = 0.000) for 2048 atoms. Found 32 (32 requested) and removed 32 (32 requested) atoms. Failed to save intermediate PDB Cycle 29: After refmac, R = 0.1915 (Rfree = 0.000) for 2041 atoms. Found 32 (32 requested) and removed 30 (32 requested) atoms. Cycle 30: After refmac, R = 0.1882 (Rfree = 0.000) for 2030 atoms. Found 32 (32 requested) and removed 26 (32 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 2.24 2.49 NCS extension: 0 residues added, 2038 seeds are put forward Round 1: 176 peptides, 3 chains. Longest chain 139 peptides. Score 0.826 Round 2: 172 peptides, 3 chains. Longest chain 79 peptides. Score 0.819 Round 3: 174 peptides, 4 chains. Longest chain 137 peptides. Score 0.812 Round 4: 175 peptides, 3 chains. Longest chain 92 peptides. Score 0.825 Round 5: 170 peptides, 5 chains. Longest chain 91 peptides. Score 0.792 Taking the results from Round 1 Chains 4, Residues 173, Estimated correctness of the model 96.8 % 3 chains (172 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 32 A and 35 A Built loop between residues 172 A and 176 A 1 chains (177 residues) following loop building 1 chains (177 residues) in sequence following loop building ------------------------------------------------------ Failed to save intermediate PDB 23087 reflections ( 99.94 % complete ) and 1991 restraints for refining 2018 atoms. 447 conditional restraints added. Observations/parameters ratio is 2.86 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2183 (Rfree = 0.000) for 2018 atoms. Found 31 (31 requested) and removed 34 (31 requested) atoms. Cycle 32: After refmac, R = 0.2042 (Rfree = 0.000) for 2006 atoms. Found 31 (31 requested) and removed 31 (31 requested) atoms. Failed to save intermediate PDB Cycle 33: After refmac, R = 0.1918 (Rfree = 0.000) for 2000 atoms. Found 31 (31 requested) and removed 30 (31 requested) atoms. Cycle 34: After refmac, R = 0.1861 (Rfree = 0.000) for 1996 atoms. Found 31 (31 requested) and removed 27 (31 requested) atoms. Failed to save intermediate PDB Cycle 35: After refmac, R = 0.1830 (Rfree = 0.000) for 1994 atoms. Found 30 (31 requested) and removed 19 (31 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 2.24 2.49 NCS extension: 0 residues added, 2006 seeds are put forward Round 1: 175 peptides, 3 chains. Longest chain 156 peptides. Score 0.825 Round 2: 175 peptides, 4 chains. Longest chain 134 peptides. Score 0.814 Round 3: 173 peptides, 4 chains. Longest chain 101 peptides. Score 0.810 Round 4: 174 peptides, 5 chains. Longest chain 82 peptides. Score 0.800 Round 5: 169 peptides, 7 chains. Longest chain 74 peptides. Score 0.766 Taking the results from Round 1 Chains 6, Residues 172, Estimated correctness of the model 96.8 % 3 chains (160 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 24 A and 35 A Built loop between residues 173 A and 180 A 2 chains (177 residues) following loop building 1 chains (176 residues) in sequence following loop building ------------------------------------------------------ 23087 reflections ( 99.94 % complete ) and 2057 restraints for refining 2019 atoms. 517 conditional restraints added. Observations/parameters ratio is 2.86 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2293 (Rfree = 0.000) for 2019 atoms. Found 31 (31 requested) and removed 37 (31 requested) atoms. Cycle 37: After refmac, R = 0.2120 (Rfree = 0.000) for 2003 atoms. Found 31 (31 requested) and removed 31 (31 requested) atoms. Cycle 38: After refmac, R = 0.1995 (Rfree = 0.000) for 1998 atoms. Found 31 (31 requested) and removed 31 (31 requested) atoms. Cycle 39: After refmac, R = 0.1960 (Rfree = 0.000) for 1992 atoms. Found 31 (31 requested) and removed 32 (31 requested) atoms. Cycle 40: After refmac, R = 0.1929 (Rfree = 0.000) for 1988 atoms. Found 31 (31 requested) and removed 29 (31 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 2.24 2.49 NCS extension: 0 residues added, 1994 seeds are put forward Round 1: 175 peptides, 4 chains. Longest chain 138 peptides. Score 0.814 Round 2: 176 peptides, 3 chains. Longest chain 139 peptides. Score 0.826 Round 3: 174 peptides, 6 chains. Longest chain 71 peptides. Score 0.789 Round 4: 175 peptides, 4 chains. Longest chain 108 peptides. Score 0.814 Round 5: 169 peptides, 5 chains. Longest chain 68 peptides. Score 0.790 Taking the results from Round 2 Chains 4, Residues 173, Estimated correctness of the model 96.8 % 3 chains (169 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 32 A and 35 A Built loop between residues 168 A and 175 A 1 chains (177 residues) following loop building 1 chains (177 residues) in sequence following loop building ------------------------------------------------------ 23087 reflections ( 99.94 % complete ) and 1930 restraints for refining 1978 atoms. 386 conditional restraints added. Observations/parameters ratio is 2.92 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2195 (Rfree = 0.000) for 1978 atoms. Found 31 (31 requested) and removed 34 (31 requested) atoms. Cycle 42: After refmac, R = 0.2037 (Rfree = 0.000) for 1966 atoms. Found 31 (31 requested) and removed 28 (31 requested) atoms. Cycle 43: After refmac, R = 0.1937 (Rfree = 0.000) for 1966 atoms. Found 31 (31 requested) and removed 19 (31 requested) atoms. Cycle 44: After refmac, R = 0.1879 (Rfree = 0.000) for 1966 atoms. Found 31 (31 requested) and removed 21 (31 requested) atoms. Cycle 45: After refmac, R = 0.1848 (Rfree = 0.000) for 1966 atoms. Found 31 (31 requested) and removed 18 (31 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 2.25 2.51 NCS extension: 0 residues added, 1980 seeds are put forward Round 1: 174 peptides, 4 chains. Longest chain 138 peptides. Score 0.812 Round 2: 175 peptides, 3 chains. Longest chain 83 peptides. Score 0.825 Round 3: 175 peptides, 5 chains. Longest chain 108 peptides. Score 0.802 Round 4: 176 peptides, 3 chains. Longest chain 86 peptides. Score 0.826 Round 5: 170 peptides, 5 chains. Longest chain 81 peptides. Score 0.792 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 4, Residues 173, Estimated correctness of the model 96.8 % 3 chains (172 residues) have been docked in sequence Sequence coverage is 98 % All DUM atoms will be removed Building loops using Loopy2018 Built loop between residues 98 A and 101 A Built loop between residues 172 A and 176 A 1 chains (177 residues) following loop building 1 chains (177 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. Update only waters. 23087 reflections ( 99.94 % complete ) and 1544 restraints for refining 1503 atoms. Observations/parameters ratio is 3.84 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2710 (Rfree = 0.000) for 1503 atoms. Found 23 (23 requested) and removed 0 (23 requested) atoms. Cycle 47: After refmac, R = 0.2445 (Rfree = 0.000) for 1503 atoms. Found 24 (24 requested) and removed 1 (24 requested) atoms. Cycle 48: After refmac, R = 0.2260 (Rfree = 0.000) for 1503 atoms. Found 24 (24 requested) and removed 0 (24 requested) atoms. Failed to save intermediate PDB Cycle 49: After refmac, R = 0.2133 (Rfree = 0.000) for 1503 atoms. Found 24 (24 requested) and removed 1 (24 requested) atoms. Writing output files ... Normal termination of warpNtrace Tue 25 Dec 20:19:27 GMT 2018 Job finished. TimeTaking 51.51