Mon 24 Dec 00:35:15 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir Job ID is set to 2op5-2.2-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2op5-2.2-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2op5-2.2-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2op5-2.2-parrot-mrncs 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/mrncs/ArpWArp/wArpResults/WorkingDir/2op5-2.2-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2op5-2.2-parrot-mrncs ############### 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 00:35:19 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/mrncs/ArpWArp/wArpResults/WorkingDir/2op5-2.2-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2op5-2.2-parrot-mrncs/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 637 and 0 Target number of residues in the AU: 637 Target solvent content: 0.5032 Checking the provided sequence file Detected sequence length: 117 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 6 Adjusted target number of residues: 702 Adjusted target solvent content: 0.45 Input MTZ file: 2op5-2.2-parrot-mrncs.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: 56.562 84.634 144.950 90.000 90.000 90.000 Input sequence file: 2op5-2.2-parrot-mrncs.fasta_lf Building free atoms model in initial map for 5616 target number of atoms Had to go as low as 0.55 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: 73.087 2.190 Wilson plot Bfac: 24.02 36536 reflections ( 99.76 % complete ) and 0 restraints for refining 6278 atoms. Observations/parameters ratio is 1.45 ------------------------------------------------------ Starting model: R = 0.3352 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2821 (Rfree = 0.000) for 6278 atoms. Found 136 (166 requested) and removed 96 (83 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 2.19 2.34 NCS extension: 0 residues added, 6318 seeds are put forward Round 1: 463 peptides, 61 chains. Longest chain 18 peptides. Score 0.639 Round 2: 525 peptides, 39 chains. Longest chain 41 peptides. Score 0.828 Round 3: 557 peptides, 36 chains. Longest chain 54 peptides. Score 0.861 Round 4: 580 peptides, 27 chains. Longest chain 75 peptides. Score 0.901 Round 5: 583 peptides, 26 chains. Longest chain 60 peptides. Score 0.905 Taking the results from Round 5 Chains 33, Residues 557, Estimated correctness of the model 98.7 % 17 chains (461 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 79 A and 82 A Built loop between residues 57 D and 62 D Built loop between residues 57 F and 66 F 28 chains (567 residues) following loop building 14 chains (475 residues) in sequence following loop building ------------------------------------------------------ 36536 reflections ( 99.76 % complete ) and 6742 restraints for refining 5692 atoms. 2352 conditional restraints added. Observations/parameters ratio is 1.60 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3051 (Rfree = 0.000) for 5692 atoms. Found 112 (150 requested) and removed 99 (75 requested) atoms. Cycle 2: After refmac, R = 0.2808 (Rfree = 0.000) for 5674 atoms. Found 76 (147 requested) and removed 76 (75 requested) atoms. Cycle 3: After refmac, R = 0.2667 (Rfree = 0.000) for 5645 atoms. Found 65 (144 requested) and removed 75 (75 requested) atoms. Cycle 4: After refmac, R = 0.2555 (Rfree = 0.000) for 5618 atoms. Found 57 (140 requested) and removed 62 (74 requested) atoms. Cycle 5: After refmac, R = 0.2468 (Rfree = 0.000) for 5598 atoms. Found 61 (136 requested) and removed 30 (74 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 2.12 2.27 NCS extension: 36 residues added (31 deleted due to clashes), 5684 seeds are put forward Round 1: 580 peptides, 25 chains. Longest chain 54 peptides. Score 0.907 Round 2: 594 peptides, 26 chains. Longest chain 57 peptides. Score 0.910 Round 3: 588 peptides, 25 chains. Longest chain 83 peptides. Score 0.910 Round 4: 590 peptides, 27 chains. Longest chain 54 peptides. Score 0.906 Round 5: 596 peptides, 21 chains. Longest chain 74 peptides. Score 0.923 Taking the results from Round 5 Chains 22, Residues 575, Estimated correctness of the model 99.1 % 15 chains (529 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 39 B and 42 B Built loop between residues 58 D and 62 D Built loop between residues 71 D and 74 D Built loop between residues 94 D and 97 D Built loop between residues 43 F and 46 F 16 chains (585 residues) following loop building 10 chains (540 residues) in sequence following loop building ------------------------------------------------------ Failed to save intermediate PDB 36536 reflections ( 99.76 % complete ) and 6446 restraints for refining 5815 atoms. 1671 conditional restraints added. Observations/parameters ratio is 1.57 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2667 (Rfree = 0.000) for 5815 atoms. Found 82 (141 requested) and removed 94 (76 requested) atoms. Cycle 7: After refmac, R = 0.2493 (Rfree = 0.000) for 5791 atoms. Found 62 (138 requested) and removed 77 (76 requested) atoms. Cycle 8: After refmac, R = 0.2367 (Rfree = 0.000) for 5767 atoms. Found 69 (134 requested) and removed 67 (76 requested) atoms. Cycle 9: After refmac, R = 0.2299 (Rfree = 0.000) for 5762 atoms. Found 56 (131 requested) and removed 41 (76 requested) atoms. Cycle 10: After refmac, R = 0.2231 (Rfree = 0.000) for 5772 atoms. Found 49 (128 requested) and removed 38 (76 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 2.11 2.26 NCS extension: 58 residues added (130 deleted due to clashes), 5847 seeds are put forward Round 1: 598 peptides, 21 chains. Longest chain 81 peptides. Score 0.924 Round 2: 609 peptides, 19 chains. Longest chain 74 peptides. Score 0.932 Round 3: 606 peptides, 25 chains. Longest chain 57 peptides. Score 0.917 Round 4: 583 peptides, 26 chains. Longest chain 57 peptides. Score 0.905 Round 5: 605 peptides, 30 chains. Longest chain 57 peptides. Score 0.904 Taking the results from Round 2 Chains 19, Residues 590, Estimated correctness of the model 99.3 % 13 chains (548 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 40 A and 43 A Built loop between residues 56 D and 61 D 17 chains (596 residues) following loop building 11 chains (554 residues) in sequence following loop building ------------------------------------------------------ 36536 reflections ( 99.76 % complete ) and 6509 restraints for refining 5878 atoms. 1641 conditional restraints added. Observations/parameters ratio is 1.55 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2401 (Rfree = 0.000) for 5878 atoms. Found 100 (127 requested) and removed 86 (77 requested) atoms. Cycle 12: After refmac, R = 0.2275 (Rfree = 0.000) for 5886 atoms. Found 68 (124 requested) and removed 77 (77 requested) atoms. Cycle 13: After refmac, R = 0.2185 (Rfree = 0.000) for 5876 atoms. Found 59 (121 requested) and removed 47 (77 requested) atoms. Cycle 14: After refmac, R = 0.2142 (Rfree = 0.000) for 5881 atoms. Found 61 (118 requested) and removed 33 (77 requested) atoms. Cycle 15: After refmac, R = 0.2097 (Rfree = 0.000) for 5904 atoms. Found 65 (115 requested) and removed 32 (78 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 2.11 2.26 NCS extension: 60 residues added (133 deleted due to clashes), 6000 seeds are put forward Round 1: 606 peptides, 19 chains. Longest chain 108 peptides. Score 0.931 Round 2: 608 peptides, 21 chains. Longest chain 108 peptides. Score 0.927 Round 3: 606 peptides, 22 chains. Longest chain 108 peptides. Score 0.924 Round 4: 606 peptides, 23 chains. Longest chain 82 peptides. Score 0.922 Round 5: 610 peptides, 20 chains. Longest chain 110 peptides. Score 0.930 Taking the results from Round 1 Chains 21, Residues 587, Estimated correctness of the model 99.3 % 12 chains (537 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 57 C and 64 C Built loop between residues 40 B and 44 B Built loop between residues 87 D and 90 D Built loop between residues 56 F and 62 F 16 chains (602 residues) following loop building 8 chains (553 residues) in sequence following loop building ------------------------------------------------------ 36536 reflections ( 99.76 % complete ) and 6631 restraints for refining 5988 atoms. 1735 conditional restraints added. Observations/parameters ratio is 1.53 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2342 (Rfree = 0.000) for 5988 atoms. Found 111 (117 requested) and removed 85 (79 requested) atoms. Cycle 17: After refmac, R = 0.2200 (Rfree = 0.000) for 6009 atoms. Found 74 (114 requested) and removed 79 (79 requested) atoms. Cycle 18: After refmac, R = 0.2121 (Rfree = 0.000) for 6001 atoms. Found 70 (111 requested) and removed 50 (79 requested) atoms. Cycle 19: After refmac, R = 0.2078 (Rfree = 0.000) for 6016 atoms. Found 72 (108 requested) and removed 37 (79 requested) atoms. Cycle 20: After refmac, R = 0.2031 (Rfree = 0.000) for 6051 atoms. Found 60 (106 requested) and removed 47 (80 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 2.10 2.25 NCS extension: 57 residues added (55 deleted due to clashes), 6125 seeds are put forward Round 1: 606 peptides, 20 chains. Longest chain 108 peptides. Score 0.929 Round 2: 608 peptides, 22 chains. Longest chain 86 peptides. Score 0.925 Round 3: 609 peptides, 19 chains. Longest chain 108 peptides. Score 0.932 Round 4: 604 peptides, 30 chains. Longest chain 86 peptides. Score 0.904 Round 5: 605 peptides, 22 chains. Longest chain 108 peptides. Score 0.924 Taking the results from Round 3 Chains 19, Residues 590, Estimated correctness of the model 99.3 % 13 chains (542 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 35 B and 38 B Built loop between residues 86 E and 91 E 17 chains (596 residues) following loop building 11 chains (548 residues) in sequence following loop building ------------------------------------------------------ 36536 reflections ( 99.76 % complete ) and 6613 restraints for refining 6029 atoms. 1764 conditional restraints added. Observations/parameters ratio is 1.52 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2281 (Rfree = 0.000) for 6029 atoms. Found 102 (102 requested) and removed 87 (79 requested) atoms. Cycle 22: After refmac, R = 0.2126 (Rfree = 0.000) for 6042 atoms. Found 78 (99 requested) and removed 61 (79 requested) atoms. Cycle 23: After refmac, R = 0.2060 (Rfree = 0.000) for 6058 atoms. Found 74 (96 requested) and removed 29 (80 requested) atoms. Cycle 24: After refmac, R = 0.2009 (Rfree = 0.000) for 6099 atoms. Found 80 (97 requested) and removed 34 (80 requested) atoms. Cycle 25: After refmac, R = 0.1964 (Rfree = 0.000) for 6141 atoms. Found 69 (97 requested) and removed 53 (81 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 2.11 2.26 NCS extension: 31 residues added (101 deleted due to clashes), 6194 seeds are put forward Round 1: 604 peptides, 21 chains. Longest chain 108 peptides. Score 0.926 Round 2: 609 peptides, 22 chains. Longest chain 107 peptides. Score 0.925 Round 3: 612 peptides, 20 chains. Longest chain 108 peptides. Score 0.931 Round 4: 599 peptides, 26 chains. Longest chain 92 peptides. Score 0.912 Round 5: 607 peptides, 25 chains. Longest chain 68 peptides. Score 0.917 Taking the results from Round 3 Chains 20, Residues 592, Estimated correctness of the model 99.3 % 15 chains (548 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 36 A and 39 A Built loop between residues 57 C and 64 C Built loop between residues 56 E and 59 E Built loop between residues 86 E and 91 E Built loop between residues 39 F and 42 F 15 chains (608 residues) following loop building 10 chains (564 residues) in sequence following loop building ------------------------------------------------------ 36536 reflections ( 99.76 % complete ) and 6550 restraints for refining 6136 atoms. 1563 conditional restraints added. Observations/parameters ratio is 1.49 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2300 (Rfree = 0.000) for 6136 atoms. Found 94 (94 requested) and removed 102 (81 requested) atoms. Cycle 27: After refmac, R = 0.2142 (Rfree = 0.000) for 6125 atoms. Found 91 (91 requested) and removed 81 (81 requested) atoms. Cycle 28: After refmac, R = 0.2051 (Rfree = 0.000) for 6135 atoms. Found 87 (87 requested) and removed 41 (81 requested) atoms. Cycle 29: After refmac, R = 0.2000 (Rfree = 0.000) for 6180 atoms. Found 75 (88 requested) and removed 53 (81 requested) atoms. Cycle 30: After refmac, R = 0.1972 (Rfree = 0.000) for 6199 atoms. Found 83 (85 requested) and removed 53 (82 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 2.10 2.25 NCS extension: 13 residues added (23 deleted due to clashes), 6248 seeds are put forward Round 1: 609 peptides, 18 chains. Longest chain 56 peptides. Score 0.934 Round 2: 611 peptides, 19 chains. Longest chain 74 peptides. Score 0.933 Round 3: 615 peptides, 17 chains. Longest chain 108 peptides. Score 0.938 Round 4: 603 peptides, 24 chains. Longest chain 92 peptides. Score 0.918 Round 5: 610 peptides, 22 chains. Longest chain 89 peptides. Score 0.926 Taking the results from Round 3 Chains 21, Residues 598, Estimated correctness of the model 99.4 % 13 chains (560 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 36 A and 39 A Built loop between residues 57 B and 62 B Built loop between residues 36 F and 39 F Built loop between residues 55 F and 61 F 15 chains (608 residues) following loop building 9 chains (573 residues) in sequence following loop building ------------------------------------------------------ 36536 reflections ( 99.76 % complete ) and 6427 restraints for refining 6164 atoms. 1407 conditional restraints added. Observations/parameters ratio is 1.48 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2219 (Rfree = 0.000) for 6164 atoms. Found 81 (81 requested) and removed 90 (81 requested) atoms. Cycle 32: After refmac, R = 0.2083 (Rfree = 0.000) for 6147 atoms. Found 81 (81 requested) and removed 81 (81 requested) atoms. Cycle 33: After refmac, R = 0.2020 (Rfree = 0.000) for 6141 atoms. Found 81 (81 requested) and removed 45 (81 requested) atoms. Cycle 34: After refmac, R = 0.1987 (Rfree = 0.000) for 6172 atoms. Found 75 (81 requested) and removed 30 (81 requested) atoms. Failed to save intermediate PDB Cycle 35: After refmac, R = 0.1949 (Rfree = 0.000) for 6215 atoms. Found 76 (82 requested) and removed 47 (82 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 2.10 2.25 NCS extension: 56 residues added (58 deleted due to clashes), 6305 seeds are put forward Round 1: 614 peptides, 20 chains. Longest chain 108 peptides. Score 0.931 Round 2: 616 peptides, 18 chains. Longest chain 108 peptides. Score 0.936 Round 3: 615 peptides, 20 chains. Longest chain 87 peptides. Score 0.932 Round 4: 611 peptides, 22 chains. Longest chain 87 peptides. Score 0.926 Round 5: 613 peptides, 22 chains. Longest chain 95 peptides. Score 0.927 Taking the results from Round 2 Chains 19, Residues 598, Estimated correctness of the model 99.4 % 11 chains (532 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 36 A and 39 A Built loop between residues 57 A and 61 A Built loop between residues 45 C and 48 C Built loop between residues 58 B and 61 B 15 chains (607 residues) following loop building 7 chains (541 residues) in sequence following loop building ------------------------------------------------------ 36536 reflections ( 99.76 % complete ) and 6639 restraints for refining 6150 atoms. 1758 conditional restraints added. Observations/parameters ratio is 1.49 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2184 (Rfree = 0.000) for 6150 atoms. Found 81 (81 requested) and removed 90 (81 requested) atoms. Cycle 37: After refmac, R = 0.2069 (Rfree = 0.000) for 6137 atoms. Found 81 (81 requested) and removed 69 (81 requested) atoms. Cycle 38: After refmac, R = 0.2007 (Rfree = 0.000) for 6147 atoms. Found 81 (81 requested) and removed 27 (81 requested) atoms. Cycle 39: After refmac, R = 0.1970 (Rfree = 0.000) for 6200 atoms. Found 60 (82 requested) and removed 41 (82 requested) atoms. Cycle 40: After refmac, R = 0.1924 (Rfree = 0.000) for 6215 atoms. Found 73 (82 requested) and removed 28 (82 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 2.10 2.25 NCS extension: 19 residues added (98 deleted due to clashes), 6281 seeds are put forward Round 1: 613 peptides, 22 chains. Longest chain 103 peptides. Score 0.927 Round 2: 617 peptides, 19 chains. Longest chain 109 peptides. Score 0.934 Round 3: 615 peptides, 22 chains. Longest chain 68 peptides. Score 0.927 Round 4: 617 peptides, 21 chains. Longest chain 109 peptides. Score 0.930 Round 5: 607 peptides, 27 chains. Longest chain 68 peptides. Score 0.913 Taking the results from Round 2 Chains 20, Residues 598, Estimated correctness of the model 99.3 % 13 chains (544 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 57 A and 61 A Built loop between residues 56 C and 61 C Built loop between residues 57 B and 60 B Built loop between residues 71 B and 74 B Built loop between residues 59 E and 63 E Built loop between residues 57 F and 61 F Built loop between residues 71 F and 78 F 12 chains (620 residues) following loop building 6 chains (567 residues) in sequence following loop building ------------------------------------------------------ 36536 reflections ( 99.76 % complete ) and 6555 restraints for refining 6255 atoms. 1496 conditional restraints added. Observations/parameters ratio is 1.46 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2252 (Rfree = 0.000) for 6255 atoms. Found 82 (82 requested) and removed 91 (82 requested) atoms. Cycle 42: After refmac, R = 0.2121 (Rfree = 0.000) for 6239 atoms. Found 82 (82 requested) and removed 82 (82 requested) atoms. Cycle 43: After refmac, R = 0.2041 (Rfree = 0.000) for 6237 atoms. Found 82 (82 requested) and removed 63 (82 requested) atoms. Cycle 44: After refmac, R = 0.1995 (Rfree = 0.000) for 6254 atoms. Found 82 (82 requested) and removed 54 (82 requested) atoms. Cycle 45: After refmac, R = 0.1965 (Rfree = 0.000) for 6281 atoms. Found 79 (83 requested) and removed 64 (83 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 2.09 2.23 NCS extension: 50 residues added (41 deleted due to clashes), 6354 seeds are put forward Round 1: 607 peptides, 22 chains. Longest chain 107 peptides. Score 0.925 Round 2: 611 peptides, 20 chains. Longest chain 107 peptides. Score 0.930 Round 3: 616 peptides, 21 chains. Longest chain 67 peptides. Score 0.930 Round 4: 613 peptides, 19 chains. Longest chain 108 peptides. Score 0.933 Round 5: 610 peptides, 26 chains. Longest chain 73 peptides. Score 0.916 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 20, Residues 594, Estimated correctness of the model 99.3 % 13 chains (552 residues) have been docked in sequence Sequence coverage is 92 % All DUM atoms will be removed Building loops using Loopy2018 Built loop between residues 36 A and 42 A Built loop between residues 81 A and 93 A Built loop between residues 56 C and 62 C Built loop between residues 45 B and 48 B 16 chains (617 residues) following loop building 9 chains (575 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. Update only waters. Failed to save intermediate PDB 36536 reflections ( 99.76 % complete ) and 5054 restraints for refining 4971 atoms. Observations/parameters ratio is 1.84 ------------------------------------------------------ Cycle 46: After refmac, R = 0.3068 (Rfree = 0.000) for 4971 atoms. Found 30 (65 requested) and removed 0 (65 requested) atoms. Cycle 47: After refmac, R = 0.2959 (Rfree = 0.000) for 4971 atoms. Found 11 (66 requested) and removed 0 (66 requested) atoms. Cycle 48: After refmac, R = 0.2900 (Rfree = 0.000) for 4971 atoms. Found 5 (66 requested) and removed 2 (66 requested) atoms. Cycle 49: After refmac, R = 0.2866 (Rfree = 0.000) for 4971 atoms. TimeTaking 67.55