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 1vqy-2.4-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/1vqy-2.4-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/1vqy-2.4-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vqy-2.4-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/1vqy-2.4-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vqy-2.4-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/1vqy-2.4-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vqy-2.4-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 973 and 0 Target number of residues in the AU: 973 Target solvent content: 0.4624 Checking the provided sequence file Detected sequence length: 116 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 8 Adjusted target number of residues: 928 Adjusted target solvent content: 0.49 Input MTZ file: 1vqy-2.4-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: 19 Cell parameters: 68.026 110.931 129.804 90.000 90.000 90.000 Input sequence file: 1vqy-2.4-parrot-hancs.fasta_lf Building free atoms model in initial map for 7424 target number of atoms Had to go as low as 0.50 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: 29.074 2.400 Wilson plot Bfac: 16.49 38307 reflections ( 97.84 % complete ) and 0 restraints for refining 8196 atoms. Observations/parameters ratio is 1.17 ------------------------------------------------------ Starting model: R = 0.2957 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2169 (Rfree = 0.000) for 8196 atoms. Found 135 (167 requested) and removed 99 (83 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 2.01 2.04 NCS extension: 0 residues added, 8232 seeds are put forward Round 1: 584 peptides, 76 chains. Longest chain 26 peptides. Score 0.612 Round 2: 694 peptides, 59 chains. Longest chain 32 peptides. Score 0.786 Round 3: 745 peptides, 43 chains. Longest chain 68 peptides. Score 0.862 Round 4: 762 peptides, 37 chains. Longest chain 104 peptides. Score 0.883 Round 5: 766 peptides, 29 chains. Longest chain 103 peptides. Score 0.902 Taking the results from Round 5 Chains 32, Residues 737, Estimated correctness of the model 98.2 % 21 chains (685 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 53 A and 56 A Built loop between residues 72 A and 75 A Built loop between residues 71 B and 74 B Built loop between residues 95 B and 99 B Built loop between residues 26 G and 30 G Built loop between residues 81 G and 87 G Built loop between residues 31 H and 38 H Built loop between residues 79 H and 82 H 24 chains (761 residues) following loop building 13 chains (710 residues) in sequence following loop building ------------------------------------------------------ 38307 reflections ( 97.84 % complete ) and 8555 restraints for refining 7563 atoms. 2534 conditional restraints added. Observations/parameters ratio is 1.27 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2681 (Rfree = 0.000) for 7563 atoms. Found 154 (154 requested) and removed 107 (77 requested) atoms. Failed to save intermediate PDB Cycle 2: After refmac, R = 0.2453 (Rfree = 0.000) for 7559 atoms. Found 129 (152 requested) and removed 78 (77 requested) atoms. Cycle 3: After refmac, R = 0.2329 (Rfree = 0.000) for 7583 atoms. Found 102 (149 requested) and removed 78 (77 requested) atoms. Cycle 4: After refmac, R = 0.2240 (Rfree = 0.000) for 7578 atoms. Found 107 (145 requested) and removed 55 (77 requested) atoms. Cycle 5: After refmac, R = 0.2187 (Rfree = 0.000) for 7613 atoms. Found 75 (143 requested) and removed 64 (77 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 2.01 2.04 NCS extension: 53 residues added (176 deleted due to clashes), 7695 seeds are put forward Round 1: 816 peptides, 19 chains. Longest chain 104 peptides. Score 0.935 Round 2: 821 peptides, 14 chains. Longest chain 104 peptides. Score 0.944 Round 3: 826 peptides, 15 chains. Longest chain 104 peptides. Score 0.943 Round 4: 825 peptides, 14 chains. Longest chain 106 peptides. Score 0.945 Round 5: 826 peptides, 16 chains. Longest chain 105 peptides. Score 0.942 Taking the results from Round 4 Chains 17, Residues 811, Estimated correctness of the model 99.4 % 11 chains (778 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 71 F and 75 F 16 chains (814 residues) following loop building 10 chains (781 residues) in sequence following loop building ------------------------------------------------------ 38307 reflections ( 97.84 % complete ) and 7823 restraints for refining 7652 atoms. 1229 conditional restraints added. Observations/parameters ratio is 1.25 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2444 (Rfree = 0.000) for 7652 atoms. Found 139 (139 requested) and removed 94 (77 requested) atoms. Failed to save intermediate PDB Cycle 7: After refmac, R = 0.2220 (Rfree = 0.000) for 7672 atoms. Found 103 (137 requested) and removed 79 (78 requested) atoms. Cycle 8: After refmac, R = 0.2136 (Rfree = 0.000) for 7677 atoms. Found 77 (134 requested) and removed 78 (78 requested) atoms. Cycle 9: After refmac, R = 0.2091 (Rfree = 0.000) for 7657 atoms. Found 97 (131 requested) and removed 80 (78 requested) atoms. Cycle 10: After refmac, R = 0.2046 (Rfree = 0.000) for 7660 atoms. Found 93 (128 requested) and removed 77 (78 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 2.03 2.06 NCS extension: 10 residues added (123 deleted due to clashes), 7689 seeds are put forward Round 1: 824 peptides, 15 chains. Longest chain 104 peptides. Score 0.943 Round 2: 833 peptides, 10 chains. Longest chain 106 peptides. Score 0.952 Round 3: 825 peptides, 14 chains. Longest chain 105 peptides. Score 0.945 Round 4: 814 peptides, 17 chains. Longest chain 105 peptides. Score 0.938 Round 5: 815 peptides, 17 chains. Longest chain 101 peptides. Score 0.938 Taking the results from Round 2 Chains 14, Residues 823, Estimated correctness of the model 99.5 % 10 chains (810 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 46 F and 52 F 12 chains (824 residues) following loop building 9 chains (815 residues) in sequence following loop building ------------------------------------------------------ Failed to save intermediate PDB 38307 reflections ( 97.84 % complete ) and 7482 restraints for refining 7615 atoms. 693 conditional restraints added. Observations/parameters ratio is 1.26 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2145 (Rfree = 0.000) for 7615 atoms. Found 124 (124 requested) and removed 85 (77 requested) atoms. Cycle 12: After refmac, R = 0.2027 (Rfree = 0.000) for 7639 atoms. Found 114 (121 requested) and removed 78 (77 requested) atoms. Failed to save intermediate PDB Cycle 13: After refmac, R = 0.1961 (Rfree = 0.000) for 7665 atoms. Found 90 (119 requested) and removed 80 (78 requested) atoms. Cycle 14: After refmac, R = 0.1935 (Rfree = 0.000) for 7658 atoms. Found 95 (115 requested) and removed 79 (78 requested) atoms. Failed to save intermediate PDB Cycle 15: After refmac, R = 0.1912 (Rfree = 0.000) for 7665 atoms. Found 103 (112 requested) and removed 82 (78 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 2.02 2.05 NCS extension: 0 residues added (40 deleted due to clashes), 7690 seeds are put forward Round 1: 821 peptides, 16 chains. Longest chain 104 peptides. Score 0.941 Round 2: 828 peptides, 11 chains. Longest chain 105 peptides. Score 0.950 Round 3: 825 peptides, 15 chains. Longest chain 105 peptides. Score 0.943 Round 4: 821 peptides, 18 chains. Longest chain 105 peptides. Score 0.937 Round 5: 824 peptides, 15 chains. Longest chain 108 peptides. Score 0.943 Taking the results from Round 2 Chains 13, Residues 817, Estimated correctness of the model 99.5 % 11 chains (809 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 71 A and 74 A Built loop between residues 25 B and 28 B Built loop between residues 56 F and 59 F 10 chains (823 residues) following loop building 8 chains (815 residues) in sequence following loop building ------------------------------------------------------ 38307 reflections ( 97.84 % complete ) and 7487 restraints for refining 7591 atoms. 703 conditional restraints added. Observations/parameters ratio is 1.26 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2112 (Rfree = 0.000) for 7591 atoms. Found 108 (108 requested) and removed 85 (77 requested) atoms. Cycle 17: After refmac, R = 0.1961 (Rfree = 0.000) for 7609 atoms. Found 105 (105 requested) and removed 78 (77 requested) atoms. Cycle 18: After refmac, R = 0.2052 (Rfree = 0.000) for 7625 atoms. Found 102 (102 requested) and removed 78 (77 requested) atoms. Cycle 19: After refmac, R = 0.1966 (Rfree = 0.000) for 7638 atoms. Found 99 (99 requested) and removed 48 (77 requested) atoms. Cycle 20: After refmac, R = 0.1916 (Rfree = 0.000) for 7668 atoms. Found 87 (100 requested) and removed 56 (78 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 2.01 2.04 NCS extension: 0 residues added (7 deleted due to clashes), 7706 seeds are put forward Round 1: 827 peptides, 17 chains. Longest chain 105 peptides. Score 0.940 Round 2: 827 peptides, 11 chains. Longest chain 105 peptides. Score 0.950 Round 3: 824 peptides, 17 chains. Longest chain 105 peptides. Score 0.940 Round 4: 824 peptides, 15 chains. Longest chain 104 peptides. Score 0.943 Round 5: 824 peptides, 16 chains. Longest chain 104 peptides. Score 0.941 Taking the results from Round 2 Chains 13, Residues 816, Estimated correctness of the model 99.5 % 11 chains (811 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 59 C and 62 C Built loop between residues 26 B and 29 B Built loop between residues 87 B and 90 B 10 chains (822 residues) following loop building 8 chains (817 residues) in sequence following loop building ------------------------------------------------------ 38307 reflections ( 97.84 % complete ) and 7448 restraints for refining 7617 atoms. 659 conditional restraints added. Observations/parameters ratio is 1.26 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2013 (Rfree = 0.000) for 7617 atoms. Found 96 (96 requested) and removed 82 (77 requested) atoms. Cycle 22: After refmac, R = 0.1934 (Rfree = 0.000) for 7617 atoms. Found 93 (93 requested) and removed 77 (77 requested) atoms. Cycle 23: After refmac, R = 0.1911 (Rfree = 0.000) for 7624 atoms. Found 90 (90 requested) and removed 75 (77 requested) atoms. Cycle 24: After refmac, R = 0.1883 (Rfree = 0.000) for 7637 atoms. Found 87 (87 requested) and removed 57 (77 requested) atoms. Cycle 25: After refmac, R = 0.1868 (Rfree = 0.000) for 7657 atoms. Found 83 (84 requested) and removed 71 (78 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 2.01 2.04 NCS extension: 0 residues added, 7672 seeds are put forward Round 1: 824 peptides, 19 chains. Longest chain 70 peptides. Score 0.936 Round 2: 823 peptides, 12 chains. Longest chain 105 peptides. Score 0.947 Round 3: 817 peptides, 14 chains. Longest chain 103 peptides. Score 0.943 Round 4: 817 peptides, 20 chains. Longest chain 104 peptides. Score 0.933 Round 5: 822 peptides, 17 chains. Longest chain 106 peptides. Score 0.939 Taking the results from Round 2 Chains 14, Residues 811, Estimated correctness of the model 99.4 % 12 chains (806 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 25 C and 28 C Built loop between residues 87 C and 90 C Built loop between residues 59 B and 62 B Built loop between residues 54 G and 57 G 10 chains (819 residues) following loop building 8 chains (814 residues) in sequence following loop building ------------------------------------------------------ 38307 reflections ( 97.84 % complete ) and 7483 restraints for refining 7604 atoms. 721 conditional restraints added. Observations/parameters ratio is 1.26 ------------------------------------------------------ Cycle 26: After refmac, R = 0.1970 (Rfree = 0.000) for 7604 atoms. Found 80 (80 requested) and removed 82 (77 requested) atoms. Cycle 27: After refmac, R = 0.1912 (Rfree = 0.000) for 7594 atoms. Found 77 (77 requested) and removed 77 (77 requested) atoms. Failed to save intermediate PDB Cycle 28: After refmac, R = 0.1871 (Rfree = 0.000) for 7585 atoms. Found 77 (77 requested) and removed 63 (77 requested) atoms. Failed to save intermediate PDB Cycle 29: After refmac, R = 0.1856 (Rfree = 0.000) for 7594 atoms. Found 77 (77 requested) and removed 71 (77 requested) atoms. Failed to save intermediate PDB Cycle 30: After refmac, R = 0.1839 (Rfree = 0.000) for 7593 atoms. Found 77 (77 requested) and removed 58 (77 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 2.01 2.04 NCS extension: 0 residues added, 7613 seeds are put forward Round 1: 822 peptides, 18 chains. Longest chain 104 peptides. Score 0.938 Round 2: 822 peptides, 11 chains. Longest chain 105 peptides. Score 0.949 Round 3: 822 peptides, 16 chains. Longest chain 105 peptides. Score 0.941 Round 4: 817 peptides, 15 chains. Longest chain 105 peptides. Score 0.941 Round 5: 815 peptides, 17 chains. Longest chain 104 peptides. Score 0.938 Taking the results from Round 2 Chains 12, Residues 811, Estimated correctness of the model 99.5 % 11 chains (807 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 87 C and 90 C Built loop between residues 58 B and 62 B Built loop between residues 71 H and 74 H 9 chains (818 residues) following loop building 8 chains (814 residues) in sequence following loop building ------------------------------------------------------ 38307 reflections ( 97.84 % complete ) and 7479 restraints for refining 7592 atoms. 720 conditional restraints added. Observations/parameters ratio is 1.26 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1959 (Rfree = 0.000) for 7592 atoms. Found 77 (77 requested) and removed 81 (77 requested) atoms. Cycle 32: After refmac, R = 0.1878 (Rfree = 0.000) for 7583 atoms. Found 77 (77 requested) and removed 78 (77 requested) atoms. Cycle 33: After refmac, R = 0.1855 (Rfree = 0.000) for 7575 atoms. Found 77 (77 requested) and removed 70 (77 requested) atoms. Cycle 34: After refmac, R = 0.1839 (Rfree = 0.000) for 7579 atoms. Found 77 (77 requested) and removed 70 (77 requested) atoms. Cycle 35: After refmac, R = 0.1833 (Rfree = 0.000) for 7575 atoms. Found 77 (77 requested) and removed 57 (77 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 2.02 2.05 NCS extension: 0 residues added, 7596 seeds are put forward Round 1: 816 peptides, 19 chains. Longest chain 105 peptides. Score 0.935 Round 2: 824 peptides, 12 chains. Longest chain 105 peptides. Score 0.948 Round 3: 825 peptides, 14 chains. Longest chain 105 peptides. Score 0.945 Round 4: 821 peptides, 15 chains. Longest chain 105 peptides. Score 0.942 Round 5: 822 peptides, 19 chains. Longest chain 105 peptides. Score 0.936 Taking the results from Round 2 Chains 14, Residues 812, Estimated correctness of the model 99.4 % 12 chains (806 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 71 A and 74 A Built loop between residues 32 C and 36 C Built loop between residues 45 B and 48 B Built loop between residues 63 H and 66 H 10 chains (821 residues) following loop building 8 chains (815 residues) in sequence following loop building ------------------------------------------------------ 38307 reflections ( 97.84 % complete ) and 7440 restraints for refining 7561 atoms. 666 conditional restraints added. Observations/parameters ratio is 1.27 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1950 (Rfree = 0.000) for 7561 atoms. Found 77 (77 requested) and removed 86 (77 requested) atoms. Cycle 37: After refmac, R = 0.1884 (Rfree = 0.000) for 7546 atoms. Found 76 (76 requested) and removed 76 (76 requested) atoms. Failed to save intermediate PDB Cycle 38: After refmac, R = 0.1863 (Rfree = 0.000) for 7540 atoms. Found 76 (76 requested) and removed 48 (76 requested) atoms. Cycle 39: After refmac, R = 0.1842 (Rfree = 0.000) for 7564 atoms. Found 77 (77 requested) and removed 62 (77 requested) atoms. Cycle 40: After refmac, R = 0.1836 (Rfree = 0.000) for 7574 atoms. Found 77 (77 requested) and removed 58 (77 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 2.00 2.03 NCS extension: 0 residues added, 7595 seeds are put forward Round 1: 825 peptides, 16 chains. Longest chain 105 peptides. Score 0.941 Round 2: 827 peptides, 11 chains. Longest chain 105 peptides. Score 0.950 Round 3: 832 peptides, 10 chains. Longest chain 105 peptides. Score 0.952 Round 4: 822 peptides, 14 chains. Longest chain 105 peptides. Score 0.944 Round 5: 819 peptides, 16 chains. Longest chain 105 peptides. Score 0.940 Taking the results from Round 3 Chains 12, Residues 822, Estimated correctness of the model 99.5 % 10 chains (817 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 45 B and 48 B Built loop between residues 57 H and 60 H 9 chains (825 residues) following loop building 8 chains (821 residues) in sequence following loop building ------------------------------------------------------ 38307 reflections ( 97.84 % complete ) and 7421 restraints for refining 7576 atoms. 600 conditional restraints added. Observations/parameters ratio is 1.26 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1982 (Rfree = 0.000) for 7576 atoms. Found 77 (77 requested) and removed 88 (77 requested) atoms. Cycle 42: After refmac, R = 0.1892 (Rfree = 0.000) for 7557 atoms. Found 77 (77 requested) and removed 77 (77 requested) atoms. Failed to save intermediate PDB Cycle 43: After refmac, R = 0.1862 (Rfree = 0.000) for 7551 atoms. Found 76 (76 requested) and removed 59 (76 requested) atoms. Cycle 44: After refmac, R = 0.1862 (Rfree = 0.000) for 7563 atoms. Found 77 (77 requested) and removed 56 (77 requested) atoms. Failed to save intermediate PDB Cycle 45: After refmac, R = 0.1839 (Rfree = 0.000) for 7579 atoms. Found 77 (77 requested) and removed 66 (77 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 2.00 2.03 NCS extension: 0 residues added, 7592 seeds are put forward Round 1: 827 peptides, 14 chains. Longest chain 104 peptides. Score 0.945 Round 2: 834 peptides, 9 chains. Longest chain 105 peptides. Score 0.954 Round 3: 828 peptides, 15 chains. Longest chain 105 peptides. Score 0.944 Round 4: 822 peptides, 15 chains. Longest chain 105 peptides. Score 0.942 Round 5: 825 peptides, 14 chains. Longest chain 105 peptides. Score 0.945 Taking the results from Round 2 Last building cycle: Chain fragments will be rearranged Chains 11, Residues 825, Estimated correctness of the model 99.5 % 9 chains (820 residues) have been docked in sequence Sequence coverage is 99 % All DUM atoms will be removed Building loops using Loopy2018 Built loop between residues 45 B and 48 B 9 chains (826 residues) following loop building 8 chains (822 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. Update only waters. 38307 reflections ( 97.84 % complete ) and 6829 restraints for refining 6703 atoms. Observations/parameters ratio is 1.43 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2491 (Rfree = 0.000) for 6703 atoms. Found 60 (68 requested) and removed 0 (68 requested) atoms. Cycle 47: After refmac, R = 0.2367 (Rfree = 0.000) for 6703 atoms. Found 33 (68 requested) and removed 5 (68 requested) atoms. Cycle 48: After refmac, R = 0.2318 (Rfree = 0.000) for 6703 atoms. Found 18 (69 requested) and removed 3 (69 requested) atoms. Cycle 49: After refmac, R = 0.2294 (Rfree = 0.000) for 6703 atoms. Found 13 (69 requested) and removed 4 (69 requested) atoms. Writing output files ... Failed to save intermediate PDB TimeTaking 130.13