null Mon 24 Dec 07:28:32 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir Job ID is set to 2pgc-2.5-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/2pgc-2.5-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/2pgc-2.5-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2pgc-2.5-parrot-noncs 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/noncs/ArpWArp/wArpResults/WorkingDir/2pgc-2.5-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2pgc-2.5-parrot-noncs ############### 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 ============================================================ Mon 24 Dec 07:28:36 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/noncs/ArpWArp/wArpResults/WorkingDir/2pgc-2.5-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2pgc-2.5-parrot-noncs/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 874 and 0 Target number of residues in the AU: 874 Target solvent content: 0.5950 Checking the provided sequence file Detected sequence length: 207 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 5 Adjusted target number of residues: 1035 Adjusted target solvent content: 0.52 Input MTZ file: 2pgc-2.5-parrot-noncs.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: 18 Cell parameters: 137.477 139.862 60.737 90.000 90.000 90.000 Input sequence file: 2pgc-2.5-parrot-noncs.fasta_lf Building free atoms model in initial map for 8280 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: 98.043 2.530 Wilson plot Bfac: 50.47 36493 reflections ( 98.58 % complete ) and 0 restraints for refining 9212 atoms. Observations/parameters ratio is 0.99 ------------------------------------------------------ Starting model: R = 0.3413 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3039 (Rfree = 0.000) for 9212 atoms. Found 120 (161 requested) and removed 109 (80 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 2.81 2.74 NCS extension: 0 residues added, 9223 seeds are put forward Round 1: 518 peptides, 85 chains. Longest chain 16 peptides. Score 0.435 Round 2: 585 peptides, 76 chains. Longest chain 21 peptides. Score 0.564 Round 3: 650 peptides, 78 chains. Longest chain 29 peptides. Score 0.622 Round 4: 665 peptides, 73 chains. Longest chain 26 peptides. Score 0.657 Round 5: 696 peptides, 68 chains. Longest chain 37 peptides. Score 0.704 Taking the results from Round 5 Chains 75, Residues 628, Estimated correctness of the model 83.8 % 16 chains (232 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 31 B and 37 B 74 chains (630 residues) following loop building 15 chains (237 residues) in sequence following loop building ------------------------------------------------------ 36493 reflections ( 98.58 % complete ) and 14149 restraints for refining 7742 atoms. 10868 conditional restraints added. Observations/parameters ratio is 1.18 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3077 (Rfree = 0.000) for 7742 atoms. Found 127 (135 requested) and removed 87 (67 requested) atoms. Cycle 2: After refmac, R = 0.2841 (Rfree = 0.000) for 7718 atoms. Found 58 (133 requested) and removed 75 (68 requested) atoms. Cycle 3: After refmac, R = 0.2747 (Rfree = 0.000) for 7665 atoms. Found 33 (130 requested) and removed 67 (67 requested) atoms. Cycle 4: After refmac, R = 0.2723 (Rfree = 0.000) for 7601 atoms. Found 38 (125 requested) and removed 67 (66 requested) atoms. Cycle 5: After refmac, R = 0.2617 (Rfree = 0.000) for 7555 atoms. Found 42 (121 requested) and removed 66 (66 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 2.77 2.70 NCS extension: 153 residues added (82 deleted due to clashes), 7739 seeds are put forward Round 1: 663 peptides, 70 chains. Longest chain 37 peptides. Score 0.668 Round 2: 717 peptides, 65 chains. Longest chain 38 peptides. Score 0.731 Round 3: 731 peptides, 56 chains. Longest chain 38 peptides. Score 0.770 Round 4: 728 peptides, 62 chains. Longest chain 40 peptides. Score 0.749 Round 5: 737 peptides, 55 chains. Longest chain 42 peptides. Score 0.777 Taking the results from Round 5 Chains 62, Residues 682, Estimated correctness of the model 90.4 % 14 chains (346 residues) have been docked in sequence Building loops using Loopy2018 62 chains (682 residues) following loop building 14 chains (346 residues) in sequence following loop building ------------------------------------------------------ 36493 reflections ( 98.58 % complete ) and 12913 restraints for refining 7746 atoms. 8953 conditional restraints added. Observations/parameters ratio is 1.18 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2792 (Rfree = 0.000) for 7746 atoms. Found 100 (121 requested) and removed 81 (67 requested) atoms. Cycle 7: After refmac, R = 0.2612 (Rfree = 0.000) for 7739 atoms. Found 48 (120 requested) and removed 72 (68 requested) atoms. Cycle 8: After refmac, R = 0.2584 (Rfree = 0.000) for 7684 atoms. Found 55 (116 requested) and removed 70 (67 requested) atoms. Cycle 9: After refmac, R = 0.2543 (Rfree = 0.000) for 7653 atoms. Found 44 (113 requested) and removed 69 (67 requested) atoms. Cycle 10: After refmac, R = 0.2530 (Rfree = 0.000) for 7617 atoms. Found 59 (109 requested) and removed 66 (66 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 2.75 2.68 NCS extension: 267 residues added (142 deleted due to clashes), 7904 seeds are put forward Round 1: 713 peptides, 59 chains. Longest chain 41 peptides. Score 0.749 Round 2: 735 peptides, 55 chains. Longest chain 36 peptides. Score 0.776 Round 3: 750 peptides, 55 chains. Longest chain 41 peptides. Score 0.785 Round 4: 763 peptides, 52 chains. Longest chain 41 peptides. Score 0.802 Round 5: 739 peptides, 53 chains. Longest chain 36 peptides. Score 0.785 Taking the results from Round 4 Chains 62, Residues 711, Estimated correctness of the model 92.3 % 15 chains (358 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 147 E and 155 E 61 chains (707 residues) following loop building 14 chains (365 residues) in sequence following loop building ------------------------------------------------------ 36493 reflections ( 98.58 % complete ) and 12585 restraints for refining 7745 atoms. 8562 conditional restraints added. Observations/parameters ratio is 1.18 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2714 (Rfree = 0.000) for 7745 atoms. Found 94 (108 requested) and removed 73 (67 requested) atoms. Cycle 12: After refmac, R = 0.2586 (Rfree = 0.000) for 7743 atoms. Found 82 (106 requested) and removed 73 (68 requested) atoms. Cycle 13: After refmac, R = 0.2515 (Rfree = 0.000) for 7735 atoms. Found 60 (103 requested) and removed 67 (67 requested) atoms. Cycle 14: After refmac, R = 0.2331 (Rfree = 0.000) for 7722 atoms. Found 51 (100 requested) and removed 69 (67 requested) atoms. Cycle 15: After refmac, R = 0.2348 (Rfree = 0.000) for 7692 atoms. Found 39 (97 requested) and removed 67 (67 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 2.73 2.66 NCS extension: 198 residues added (94 deleted due to clashes), 7900 seeds are put forward Round 1: 712 peptides, 58 chains. Longest chain 43 peptides. Score 0.751 Round 2: 763 peptides, 53 chains. Longest chain 54 peptides. Score 0.799 Round 3: 735 peptides, 55 chains. Longest chain 49 peptides. Score 0.776 Round 4: 752 peptides, 53 chains. Longest chain 48 peptides. Score 0.793 Round 5: 757 peptides, 51 chains. Longest chain 46 peptides. Score 0.801 Taking the results from Round 5 Chains 53, Residues 706, Estimated correctness of the model 92.2 % 15 chains (445 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 44 A and 55 A 50 chains (707 residues) following loop building 14 chains (455 residues) in sequence following loop building ------------------------------------------------------ 36493 reflections ( 98.58 % complete ) and 11468 restraints for refining 7745 atoms. 6961 conditional restraints added. Observations/parameters ratio is 1.18 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2620 (Rfree = 0.000) for 7745 atoms. Found 94 (94 requested) and removed 83 (67 requested) atoms. Cycle 17: After refmac, R = 0.2408 (Rfree = 0.000) for 7734 atoms. Found 70 (92 requested) and removed 76 (67 requested) atoms. Cycle 18: After refmac, R = 0.2301 (Rfree = 0.000) for 7717 atoms. Found 45 (89 requested) and removed 69 (67 requested) atoms. Cycle 19: After refmac, R = 0.2268 (Rfree = 0.000) for 7685 atoms. Found 48 (86 requested) and removed 68 (67 requested) atoms. Cycle 20: After refmac, R = 0.2250 (Rfree = 0.000) for 7662 atoms. Found 41 (83 requested) and removed 69 (67 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 2.73 2.66 NCS extension: 347 residues added (98 deleted due to clashes), 8026 seeds are put forward Round 1: 715 peptides, 59 chains. Longest chain 50 peptides. Score 0.750 Round 2: 750 peptides, 49 chains. Longest chain 62 peptides. Score 0.803 Round 3: 766 peptides, 50 chains. Longest chain 58 peptides. Score 0.809 Round 4: 743 peptides, 59 chains. Longest chain 38 peptides. Score 0.769 Round 5: 747 peptides, 53 chains. Longest chain 45 peptides. Score 0.790 Taking the results from Round 3 Chains 58, Residues 716, Estimated correctness of the model 92.7 % 19 chains (471 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 106 C and 115 C Built loop between residues 177 C and 187 C Built loop between residues 30 B and 39 B Built loop between residues 123 B and 133 B Built loop between residues 151 E and 156 E 50 chains (742 residues) following loop building 14 chains (509 residues) in sequence following loop building ------------------------------------------------------ 36493 reflections ( 98.58 % complete ) and 10952 restraints for refining 7744 atoms. 6098 conditional restraints added. Observations/parameters ratio is 1.18 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2574 (Rfree = 0.000) for 7744 atoms. Found 81 (81 requested) and removed 85 (67 requested) atoms. Cycle 22: After refmac, R = 0.2384 (Rfree = 0.000) for 7717 atoms. Found 72 (78 requested) and removed 68 (67 requested) atoms. Cycle 23: After refmac, R = 0.2278 (Rfree = 0.000) for 7710 atoms. Found 67 (76 requested) and removed 67 (67 requested) atoms. Cycle 24: After refmac, R = 0.2220 (Rfree = 0.000) for 7704 atoms. Found 36 (73 requested) and removed 69 (67 requested) atoms. Cycle 25: After refmac, R = 0.2212 (Rfree = 0.000) for 7661 atoms. Found 44 (70 requested) and removed 68 (67 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 2.75 2.68 NCS extension: 891 residues added (446 deleted due to clashes), 8571 seeds are put forward Round 1: 734 peptides, 56 chains. Longest chain 51 peptides. Score 0.772 Round 2: 767 peptides, 53 chains. Longest chain 43 peptides. Score 0.801 Round 3: 773 peptides, 56 chains. Longest chain 39 peptides. Score 0.796 Round 4: 786 peptides, 54 chains. Longest chain 45 peptides. Score 0.809 Round 5: 789 peptides, 47 chains. Longest chain 60 peptides. Score 0.829 Taking the results from Round 5 Chains 51, Residues 742, Estimated correctness of the model 94.1 % 16 chains (478 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 37 C and 40 C Built loop between residues 176 C and 184 C 49 chains (751 residues) following loop building 14 chains (487 residues) in sequence following loop building ------------------------------------------------------ 36493 reflections ( 98.58 % complete ) and 11213 restraints for refining 7746 atoms. 6334 conditional restraints added. Observations/parameters ratio is 1.18 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2535 (Rfree = 0.000) for 7746 atoms. Found 67 (67 requested) and removed 95 (67 requested) atoms. Cycle 27: After refmac, R = 0.2367 (Rfree = 0.000) for 7702 atoms. Found 62 (67 requested) and removed 68 (67 requested) atoms. Cycle 28: After refmac, R = 0.2285 (Rfree = 0.000) for 7683 atoms. Found 42 (67 requested) and removed 68 (67 requested) atoms. Cycle 29: After refmac, R = 0.2268 (Rfree = 0.000) for 7648 atoms. Found 37 (67 requested) and removed 67 (67 requested) atoms. Cycle 30: After refmac, R = 0.2255 (Rfree = 0.000) for 7615 atoms. Found 37 (66 requested) and removed 67 (66 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 2.75 2.68 NCS extension: 583 residues added (241 deleted due to clashes), 8181 seeds are put forward Round 1: 741 peptides, 54 chains. Longest chain 46 peptides. Score 0.783 Round 2: 738 peptides, 44 chains. Longest chain 62 peptides. Score 0.811 Round 3: 763 peptides, 53 chains. Longest chain 44 peptides. Score 0.799 Round 4: 749 peptides, 57 chains. Longest chain 46 peptides. Score 0.779 Round 5: 754 peptides, 54 chains. Longest chain 74 peptides. Score 0.791 Taking the results from Round 2 Chains 52, Residues 694, Estimated correctness of the model 92.9 % 17 chains (462 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 155 E and 159 E 50 chains (695 residues) following loop building 16 chains (465 residues) in sequence following loop building ------------------------------------------------------ 36493 reflections ( 98.58 % complete ) and 11654 restraints for refining 7746 atoms. 7130 conditional restraints added. Observations/parameters ratio is 1.18 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2498 (Rfree = 0.000) for 7746 atoms. Found 67 (67 requested) and removed 79 (67 requested) atoms. Cycle 32: After refmac, R = 0.2398 (Rfree = 0.000) for 7717 atoms. Found 67 (67 requested) and removed 70 (67 requested) atoms. Cycle 33: After refmac, R = 0.2322 (Rfree = 0.000) for 7703 atoms. Found 63 (67 requested) and removed 67 (67 requested) atoms. Cycle 34: After refmac, R = 0.2270 (Rfree = 0.000) for 7689 atoms. Found 51 (67 requested) and removed 67 (67 requested) atoms. Cycle 35: After refmac, R = 0.2229 (Rfree = 0.000) for 7665 atoms. Found 60 (67 requested) and removed 68 (67 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 2.74 2.67 NCS extension: 506 residues added (326 deleted due to clashes), 8184 seeds are put forward Round 1: 747 peptides, 49 chains. Longest chain 60 peptides. Score 0.801 Round 2: 780 peptides, 43 chains. Longest chain 74 peptides. Score 0.835 Round 3: 762 peptides, 49 chains. Longest chain 48 peptides. Score 0.810 Round 4: 776 peptides, 54 chains. Longest chain 45 peptides. Score 0.803 Round 5: 759 peptides, 52 chains. Longest chain 47 peptides. Score 0.799 Taking the results from Round 2 Chains 45, Residues 737, Estimated correctness of the model 94.5 % 18 chains (534 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 30 C and 33 C Built loop between residues 109 B and 114 B Built loop between residues 178 B and 186 B 40 chains (745 residues) following loop building 15 chains (547 residues) in sequence following loop building ------------------------------------------------------ 36493 reflections ( 98.58 % complete ) and 10704 restraints for refining 7746 atoms. 5582 conditional restraints added. Observations/parameters ratio is 1.18 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2410 (Rfree = 0.000) for 7746 atoms. Found 67 (67 requested) and removed 83 (67 requested) atoms. Cycle 37: After refmac, R = 0.2262 (Rfree = 0.000) for 7714 atoms. Found 67 (67 requested) and removed 67 (67 requested) atoms. Cycle 38: After refmac, R = 0.2205 (Rfree = 0.000) for 7705 atoms. Found 46 (67 requested) and removed 68 (67 requested) atoms. Cycle 39: After refmac, R = 0.2168 (Rfree = 0.000) for 7675 atoms. Found 51 (67 requested) and removed 68 (67 requested) atoms. Cycle 40: After refmac, R = 0.2147 (Rfree = 0.000) for 7651 atoms. Found 47 (67 requested) and removed 67 (67 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 2.73 2.66 NCS extension: 340 residues added (229 deleted due to clashes), 7990 seeds are put forward Round 1: 753 peptides, 55 chains. Longest chain 51 peptides. Score 0.787 Round 2: 779 peptides, 48 chains. Longest chain 74 peptides. Score 0.821 Round 3: 774 peptides, 49 chains. Longest chain 74 peptides. Score 0.816 Round 4: 762 peptides, 59 chains. Longest chain 44 peptides. Score 0.780 Round 5: 775 peptides, 48 chains. Longest chain 76 peptides. Score 0.819 Taking the results from Round 2 Chains 53, Residues 731, Estimated correctness of the model 93.6 % 17 chains (511 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 50 C and 53 C Built loop between residues 127 D and 135 D 50 chains (737 residues) following loop building 15 chains (520 residues) in sequence following loop building ------------------------------------------------------ 36493 reflections ( 98.58 % complete ) and 11048 restraints for refining 7746 atoms. 6183 conditional restraints added. Observations/parameters ratio is 1.18 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2345 (Rfree = 0.000) for 7746 atoms. Found 67 (67 requested) and removed 82 (67 requested) atoms. Cycle 42: After refmac, R = 0.2177 (Rfree = 0.000) for 7708 atoms. Found 67 (67 requested) and removed 70 (67 requested) atoms. Cycle 43: After refmac, R = 0.2123 (Rfree = 0.000) for 7699 atoms. Found 50 (67 requested) and removed 71 (67 requested) atoms. Cycle 44: After refmac, R = 0.2100 (Rfree = 0.000) for 7672 atoms. Found 59 (67 requested) and removed 67 (67 requested) atoms. Cycle 45: After refmac, R = 0.2084 (Rfree = 0.000) for 7660 atoms. Found 43 (67 requested) and removed 68 (67 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 2.75 2.68 NCS extension: 482 residues added (468 deleted due to clashes), 8156 seeds are put forward Round 1: 751 peptides, 56 chains. Longest chain 73 peptides. Score 0.783 Round 2: 778 peptides, 43 chains. Longest chain 73 peptides. Score 0.834 Round 3: 782 peptides, 45 chains. Longest chain 52 peptides. Score 0.831 Round 4: 775 peptides, 51 chains. Longest chain 63 peptides. Score 0.811 Round 5: 783 peptides, 49 chains. Longest chain 43 peptides. Score 0.821 Taking the results from Round 2 Last building cycle: Chain fragments will be rearranged Chains 48, Residues 735, Estimated correctness of the model 94.4 % 17 chains (546 residues) have been docked in sequence Sequence coverage is 74 % Consider running further cycles of model building using 2pgc-2_warpNtrace.pdb as input Building loops using Loopy2018 Built loop between residues 110 A and 113 A Built loop between residues 119 C and 133 C Built loop between residues 127 B and 141 B Built loop between residues 109 D and 112 D 41 chains (755 residues) following loop building 13 chains (576 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 36493 reflections ( 98.58 % complete ) and 10569 restraints for refining 7745 atoms. 5358 conditional restraints added. Observations/parameters ratio is 1.18 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2307 (Rfree = 0.000) for 7745 atoms. Found 0 (67 requested) and removed 33 (67 requested) atoms. Cycle 47: After refmac, R = 0.2193 (Rfree = 0.000) for 7705 atoms. Found 0 (67 requested) and removed 8 (67 requested) atoms. Cycle 48: After refmac, R = 0.2175 (Rfree = 0.000) for 7691 atoms. Found 0 (67 requested) and removed 4 (67 requested) atoms. Cycle 49: After refmac, R = 0.2187 (Rfree = 0.000) for 7679 atoms. Found 0 (67 requested) and removed 5 (67 requested) atoms. Writing output files ... Normal termination of warpNtrace Mon 24 Dec 08:56:33 GMT 2018 Job finished. TimeTaking 88.02 Used memory is bytes: 8491056