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 2p7i-1.7-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2p7i-1.7-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2p7i-1.7-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2p7i-1.7-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/2p7i-1.7-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2p7i-1.7-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/2p7i-1.7-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2p7i-1.7-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 502 and 0 Target number of residues in the AU: 502 Target solvent content: 0.5030 Checking the provided sequence file Detected sequence length: 250 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 500 Adjusted target solvent content: 0.50 Input MTZ file: 2p7i-1.7-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: 97 Cell parameters: 120.769 120.769 149.904 90.000 90.000 90.000 Input sequence file: 2p7i-1.7-parrot-hancs.fasta_lf Building free atoms model in initial map for 4000 target number of atoms Had to go as low as 0.30 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: 94.045 1.740 Wilson plot Bfac: 23.93 56831 reflections ( 99.96 % complete ) and 0 restraints for refining 4436 atoms. Observations/parameters ratio is 3.20 ------------------------------------------------------ Starting model: R = 0.3122 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2561 (Rfree = 0.000) for 4436 atoms. Found 142 (225 requested) and removed 125 (112 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 2.01 2.01 NCS extension: 0 residues added, 4453 seeds are put forward Round 1: 345 peptides, 27 chains. Longest chain 32 peptides. Score 0.769 Round 2: 399 peptides, 17 chains. Longest chain 101 peptides. Score 0.880 Round 3: 416 peptides, 13 chains. Longest chain 108 peptides. Score 0.907 Round 4: 426 peptides, 9 chains. Longest chain 102 peptides. Score 0.927 Round 5: 431 peptides, 6 chains. Longest chain 114 peptides. Score 0.939 Taking the results from Round 5 Chains 7, Residues 425, Estimated correctness of the model 99.7 % 6 chains (420 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 80 A and 88 A Built loop between residues 148 A and 152 A Built loop between residues 91 B and 94 B 4 chains (437 residues) following loop building 3 chains (432 residues) in sequence following loop building ------------------------------------------------------ Failed to save intermediate PDB 56831 reflections ( 99.96 % complete ) and 3960 restraints for refining 3998 atoms. 403 conditional restraints added. Observations/parameters ratio is 3.55 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2681 (Rfree = 0.000) for 3998 atoms. Found 117 (203 requested) and removed 81 (101 requested) atoms. Cycle 2: After refmac, R = 0.2445 (Rfree = 0.000) for 4026 atoms. Found 97 (201 requested) and removed 20 (102 requested) atoms. Cycle 3: After refmac, R = 0.2180 (Rfree = 0.000) for 4092 atoms. Found 93 (204 requested) and removed 21 (104 requested) atoms. Failed to save intermediate PDB Cycle 4: After refmac, R = 0.2043 (Rfree = 0.000) for 4139 atoms. Found 68 (208 requested) and removed 41 (106 requested) atoms. Failed to save intermediate PDB Cycle 5: After refmac, R = 0.1949 (Rfree = 0.000) for 4148 atoms. Found 77 (204 requested) and removed 25 (106 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 1.96 1.96 NCS extension: 46 residues added (189 deleted due to clashes), 4250 seeds are put forward Round 1: 446 peptides, 7 chains. Longest chain 112 peptides. Score 0.942 Round 2: 448 peptides, 5 chains. Longest chain 165 peptides. Score 0.948 Round 3: 450 peptides, 4 chains. Longest chain 224 peptides. Score 0.952 Round 4: 448 peptides, 6 chains. Longest chain 158 peptides. Score 0.945 Round 5: 448 peptides, 6 chains. Longest chain 168 peptides. Score 0.945 Taking the results from Round 3 Chains 4, Residues 446, Estimated correctness of the model 99.8 % 4 chains (446 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 130 B and 133 B Built loop between residues 164 B and 167 B 2 chains (450 residues) following loop building 2 chains (450 residues) in sequence following loop building ------------------------------------------------------ Failed to save intermediate PDB 56831 reflections ( 99.96 % complete ) and 3987 restraints for refining 4141 atoms. 294 conditional restraints added. Observations/parameters ratio is 3.43 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2112 (Rfree = 0.000) for 4141 atoms. Found 120 (202 requested) and removed 80 (105 requested) atoms. Cycle 7: After refmac, R = 0.1962 (Rfree = 0.000) for 4175 atoms. Found 95 (199 requested) and removed 35 (106 requested) atoms. Failed to save intermediate PDB Cycle 8: After refmac, R = 0.1873 (Rfree = 0.000) for 4228 atoms. Found 94 (202 requested) and removed 51 (107 requested) atoms. Failed to save intermediate PDB Cycle 9: After refmac, R = 0.1826 (Rfree = 0.000) for 4261 atoms. Found 98 (200 requested) and removed 57 (108 requested) atoms. Cycle 10: After refmac, R = 0.1804 (Rfree = 0.000) for 4298 atoms. Found 110 (196 requested) and removed 65 (109 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 1.96 1.96 NCS extension: 5 residues added (33 deleted due to clashes), 4351 seeds are put forward Round 1: 450 peptides, 5 chains. Longest chain 178 peptides. Score 0.949 Round 2: 450 peptides, 5 chains. Longest chain 154 peptides. Score 0.949 Round 3: 451 peptides, 4 chains. Longest chain 165 peptides. Score 0.952 Round 4: 452 peptides, 4 chains. Longest chain 178 peptides. Score 0.952 Round 5: 446 peptides, 10 chains. Longest chain 106 peptides. Score 0.933 Taking the results from Round 4 Chains 7, Residues 448, Estimated correctness of the model 99.8 % 4 chains (442 residues) have been docked in sequence Building loops using Loopy2018 7 chains (448 residues) following loop building 4 chains (442 residues) in sequence following loop building ------------------------------------------------------ Failed to save intermediate PDB 56831 reflections ( 99.96 % complete ) and 4106 restraints for refining 4178 atoms. 461 conditional restraints added. Observations/parameters ratio is 3.40 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2034 (Rfree = 0.000) for 4178 atoms. Found 126 (187 requested) and removed 91 (106 requested) atoms. Cycle 12: After refmac, R = 0.1912 (Rfree = 0.000) for 4205 atoms. Found 108 (184 requested) and removed 50 (107 requested) atoms. Failed to save intermediate PDB Cycle 13: After refmac, R = 0.1841 (Rfree = 0.000) for 4260 atoms. Found 104 (187 requested) and removed 56 (108 requested) atoms. Cycle 14: After refmac, R = 0.1802 (Rfree = 0.000) for 4303 atoms. Found 98 (184 requested) and removed 59 (109 requested) atoms. Cycle 15: After refmac, R = 0.1779 (Rfree = 0.000) for 4337 atoms. Found 77 (181 requested) and removed 72 (110 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 1.95 1.95 NCS extension: 0 residues added (5 deleted due to clashes), 4347 seeds are put forward Round 1: 449 peptides, 4 chains. Longest chain 178 peptides. Score 0.951 Round 2: 451 peptides, 3 chains. Longest chain 227 peptides. Score 0.955 Round 3: 448 peptides, 5 chains. Longest chain 164 peptides. Score 0.948 Round 4: 449 peptides, 5 chains. Longest chain 120 peptides. Score 0.949 Round 5: 445 peptides, 7 chains. Longest chain 110 peptides. Score 0.941 Taking the results from Round 2 Chains 4, Residues 448, Estimated correctness of the model 99.8 % 3 chains (446 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 125 B and 128 B 3 chains (450 residues) following loop building 2 chains (448 residues) in sequence following loop building ------------------------------------------------------ Failed to save intermediate PDB 56831 reflections ( 99.96 % complete ) and 4041 restraints for refining 4196 atoms. 362 conditional restraints added. Observations/parameters ratio is 3.39 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2022 (Rfree = 0.000) for 4196 atoms. Found 145 (170 requested) and removed 79 (106 requested) atoms. Failed to save intermediate PDB Cycle 17: After refmac, R = 0.1900 (Rfree = 0.000) for 4256 atoms. Found 75 (169 requested) and removed 57 (108 requested) atoms. Cycle 18: After refmac, R = 0.1833 (Rfree = 0.000) for 4271 atoms. Found 98 (165 requested) and removed 49 (108 requested) atoms. Cycle 19: After refmac, R = 0.1795 (Rfree = 0.000) for 4312 atoms. Found 103 (166 requested) and removed 53 (109 requested) atoms. Failed to save intermediate PDB Cycle 20: After refmac, R = 0.1779 (Rfree = 0.000) for 4360 atoms. Found 83 (164 requested) and removed 76 (111 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 1.95 1.95 NCS extension: 20 residues added (241 deleted due to clashes), 4391 seeds are put forward Round 1: 449 peptides, 4 chains. Longest chain 178 peptides. Score 0.951 Round 2: 452 peptides, 3 chains. Longest chain 225 peptides. Score 0.955 Round 3: 451 peptides, 3 chains. Longest chain 227 peptides. Score 0.955 Round 4: 450 peptides, 4 chains. Longest chain 228 peptides. Score 0.952 Round 5: 448 peptides, 6 chains. Longest chain 182 peptides. Score 0.945 Taking the results from Round 3 Chains 4, Residues 448, Estimated correctness of the model 99.8 % 3 chains (446 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 125 B and 128 B 3 chains (450 residues) following loop building 2 chains (448 residues) in sequence following loop building ------------------------------------------------------ 56831 reflections ( 99.96 % complete ) and 4058 restraints for refining 4219 atoms. 379 conditional restraints added. Observations/parameters ratio is 3.37 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2006 (Rfree = 0.000) for 4219 atoms. Found 143 (154 requested) and removed 79 (107 requested) atoms. Cycle 22: After refmac, R = 0.1894 (Rfree = 0.000) for 4274 atoms. Found 89 (153 requested) and removed 54 (109 requested) atoms. Cycle 23: After refmac, R = 0.1828 (Rfree = 0.000) for 4303 atoms. Found 94 (149 requested) and removed 41 (109 requested) atoms. Cycle 24: After refmac, R = 0.1795 (Rfree = 0.000) for 4356 atoms. Found 81 (150 requested) and removed 65 (110 requested) atoms. Cycle 25: After refmac, R = 0.1774 (Rfree = 0.000) for 4367 atoms. Found 105 (147 requested) and removed 72 (111 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 1.95 1.95 NCS extension: 15 residues added (212 deleted due to clashes), 4417 seeds are put forward Round 1: 450 peptides, 4 chains. Longest chain 177 peptides. Score 0.952 Round 2: 447 peptides, 4 chains. Longest chain 224 peptides. Score 0.951 Round 3: 450 peptides, 3 chains. Longest chain 224 peptides. Score 0.955 Round 4: 448 peptides, 5 chains. Longest chain 175 peptides. Score 0.948 Round 5: 448 peptides, 5 chains. Longest chain 177 peptides. Score 0.948 Taking the results from Round 3 Chains 4, Residues 447, Estimated correctness of the model 99.8 % 3 chains (445 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 72 A and 75 A 3 chains (449 residues) following loop building 2 chains (447 residues) in sequence following loop building ------------------------------------------------------ 56831 reflections ( 99.96 % complete ) and 4076 restraints for refining 4211 atoms. 405 conditional restraints added. Observations/parameters ratio is 3.37 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2015 (Rfree = 0.000) for 4211 atoms. Found 137 (137 requested) and removed 88 (107 requested) atoms. Cycle 27: After refmac, R = 0.1894 (Rfree = 0.000) for 4253 atoms. Found 112 (134 requested) and removed 47 (108 requested) atoms. Cycle 28: After refmac, R = 0.1844 (Rfree = 0.000) for 4315 atoms. Found 90 (136 requested) and removed 60 (109 requested) atoms. Cycle 29: After refmac, R = 0.1809 (Rfree = 0.000) for 4338 atoms. Found 105 (133 requested) and removed 69 (110 requested) atoms. Cycle 30: After refmac, R = 0.1818 (Rfree = 0.000) for 4368 atoms. Found 103 (129 requested) and removed 93 (111 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 1.96 1.96 NCS extension: 18 residues added (213 deleted due to clashes), 4400 seeds are put forward Round 1: 444 peptides, 6 chains. Longest chain 175 peptides. Score 0.944 Round 2: 447 peptides, 4 chains. Longest chain 224 peptides. Score 0.951 Round 3: 448 peptides, 5 chains. Longest chain 224 peptides. Score 0.948 Round 4: 447 peptides, 5 chains. Longest chain 198 peptides. Score 0.948 Round 5: 444 peptides, 10 chains. Longest chain 89 peptides. Score 0.932 Taking the results from Round 2 Chains 5, Residues 443, Estimated correctness of the model 99.8 % 4 chains (439 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 74 B and 78 B Built loop between residues 84 B and 88 B 3 chains (449 residues) following loop building 2 chains (445 residues) in sequence following loop building ------------------------------------------------------ 56831 reflections ( 99.96 % complete ) and 4068 restraints for refining 4235 atoms. 401 conditional restraints added. Observations/parameters ratio is 3.35 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2038 (Rfree = 0.000) for 4235 atoms. Found 120 (120 requested) and removed 85 (107 requested) atoms. Cycle 32: After refmac, R = 0.1923 (Rfree = 0.000) for 4262 atoms. Found 110 (117 requested) and removed 39 (108 requested) atoms. Cycle 33: After refmac, R = 0.1865 (Rfree = 0.000) for 4330 atoms. Found 88 (119 requested) and removed 51 (110 requested) atoms. Cycle 34: After refmac, R = 0.1828 (Rfree = 0.000) for 4362 atoms. Found 88 (115 requested) and removed 59 (111 requested) atoms. Cycle 35: After refmac, R = 0.1803 (Rfree = 0.000) for 4387 atoms. Found 98 (111 requested) and removed 57 (111 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 1.96 1.96 NCS extension: 30 residues added (233 deleted due to clashes), 4462 seeds are put forward Round 1: 445 peptides, 6 chains. Longest chain 175 peptides. Score 0.944 Round 2: 448 peptides, 4 chains. Longest chain 186 peptides. Score 0.951 Round 3: 444 peptides, 6 chains. Longest chain 175 peptides. Score 0.944 Round 4: 447 peptides, 5 chains. Longest chain 228 peptides. Score 0.948 Round 5: 443 peptides, 7 chains. Longest chain 186 peptides. Score 0.941 Taking the results from Round 2 Chains 4, Residues 444, Estimated correctness of the model 99.8 % 4 chains (444 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 98 A and 102 A Built loop between residues 208 B and 212 B 2 chains (450 residues) following loop building 2 chains (450 residues) in sequence following loop building ------------------------------------------------------ 56831 reflections ( 99.96 % complete ) and 4037 restraints for refining 4250 atoms. 344 conditional restraints added. Observations/parameters ratio is 3.34 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2018 (Rfree = 0.000) for 4250 atoms. Found 108 (108 requested) and removed 95 (108 requested) atoms. Failed to save intermediate PDB Cycle 37: After refmac, R = 0.1901 (Rfree = 0.000) for 4254 atoms. Found 102 (108 requested) and removed 29 (108 requested) atoms. Cycle 38: After refmac, R = 0.1842 (Rfree = 0.000) for 4323 atoms. Found 87 (110 requested) and removed 39 (110 requested) atoms. Failed to save intermediate PDB Cycle 39: After refmac, R = 0.1816 (Rfree = 0.000) for 4366 atoms. Found 99 (111 requested) and removed 59 (111 requested) atoms. Cycle 40: After refmac, R = 0.1803 (Rfree = 0.000) for 4403 atoms. Found 92 (112 requested) and removed 88 (112 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 1.95 1.95 NCS extension: 4 residues added (0 deleted due to clashes), 4413 seeds are put forward Round 1: 450 peptides, 5 chains. Longest chain 177 peptides. Score 0.949 Round 2: 452 peptides, 2 chains. Longest chain 228 peptides. Score 0.958 Round 3: 446 peptides, 8 chains. Longest chain 177 peptides. Score 0.939 Round 4: 450 peptides, 4 chains. Longest chain 224 peptides. Score 0.952 Round 5: 448 peptides, 5 chains. Longest chain 198 peptides. Score 0.948 Taking the results from Round 2 Chains 3, Residues 450, Estimated correctness of the model 99.9 % 2 chains (447 residues) have been docked in sequence Building loops using Loopy2018 3 chains (450 residues) following loop building 2 chains (447 residues) in sequence following loop building ------------------------------------------------------ Failed to save intermediate PDB 56831 reflections ( 99.96 % complete ) and 4055 restraints for refining 4225 atoms. 376 conditional restraints added. Observations/parameters ratio is 3.36 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2003 (Rfree = 0.000) for 4225 atoms. Found 107 (107 requested) and removed 87 (107 requested) atoms. Failed to save intermediate PDB Cycle 42: After refmac, R = 0.1898 (Rfree = 0.000) for 4237 atoms. Found 108 (108 requested) and removed 37 (108 requested) atoms. Cycle 43: After refmac, R = 0.1842 (Rfree = 0.000) for 4306 atoms. Found 94 (109 requested) and removed 47 (109 requested) atoms. Failed to save intermediate PDB Cycle 44: After refmac, R = 0.1821 (Rfree = 0.000) for 4350 atoms. Found 109 (110 requested) and removed 59 (110 requested) atoms. Cycle 45: After refmac, R = 0.1808 (Rfree = 0.000) for 4395 atoms. Found 99 (111 requested) and removed 86 (111 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 1.95 1.95 NCS extension: 1 residues added (40 deleted due to clashes), 4412 seeds are put forward Round 1: 446 peptides, 7 chains. Longest chain 177 peptides. Score 0.942 Round 2: 447 peptides, 5 chains. Longest chain 183 peptides. Score 0.948 Round 3: 445 peptides, 7 chains. Longest chain 177 peptides. Score 0.941 Round 4: 441 peptides, 10 chains. Longest chain 105 peptides. Score 0.930 Round 5: 440 peptides, 12 chains. Longest chain 113 peptides. Score 0.924 Taking the results from Round 2 Last building cycle: Chain fragments will be rearranged Chains 6, Residues 442, Estimated correctness of the model 99.8 % 5 chains (438 residues) have been docked in sequence Sequence coverage is 98 % All DUM atoms will be removed Building loops using Loopy2018 Built loop between residues 76 A and 79 A Built loop between residues 84 A and 88 A Built loop between residues 205 B and 209 B 3 chains (450 residues) following loop building 2 chains (446 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. Update only waters. 56831 reflections ( 99.96 % complete ) and 3679 restraints for refining 3596 atoms. Observations/parameters ratio is 3.95 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2614 (Rfree = 0.000) for 3596 atoms. Found 91 (91 requested) and removed 0 (91 requested) atoms. Failed to save intermediate PDB Cycle 47: After refmac, R = 0.2302 (Rfree = 0.000) for 3596 atoms. Found 93 (93 requested) and removed 0 (93 requested) atoms. Cycle 48: After refmac, R = 0.2048 (Rfree = 0.000) for 3596 atoms. Found 46 (96 requested) and removed 4 (96 requested) atoms. Cycle 49: After refmac, R = 0.1933 (Rfree = 0.000) for 3596 atoms. Found 32 (97 requested) and removed 6 (97 requested) atoms. Writing output files ... Normal termination of warpNtrace Tue 25 Dec 21:09:50 GMT 2018 Job finished. Failed to save intermediate PDB TimeTaking 101.93